Correlation between copy number variation genes (focal events) and selected clinical features
Pancreatic Adenocarcinoma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C11835KZ
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/C11835KZ
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 63 focal events and 14 clinical features across 173 patients, one significant finding detected with Q value < 0.25.

  • amp_3q26.2 cnv correlated to 'Time to Death'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 63 focal events and 14 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, one significant finding 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
amp 3q26 2 30 (17%) 143 2.41e-05
(0.0213) 		0.892
(1.00) 		0.755
(1.00) 		0.577
(0.97) 		0.495
(0.97) 		0.578
(0.97) 		0.165
(0.845) 		0.913
(1.00) 		0.964
(1.00) 		0.0692
(0.745) 		0.0182
(0.593) 		0.0248
(0.593) 		0.621
(0.975) 		0.439
(0.969)
amp 1p34 2 12 (7%) 161 0.401
(0.969) 		0.00671
(0.593) 		0.634
(0.978) 		0.349
(0.947) 		0.519
(0.97) 		0.261
(0.912) 		0.551
(0.97) 		0.0186
(0.593) 		0.332
(0.947) 		0.334
(0.947) 		1
(1.00) 		0.184
(0.845)
amp 1p12 25 (14%) 148 0.527
(0.97) 		0.205
(0.845) 		0.477
(0.97) 		0.502
(0.97) 		1
(1.00) 		0.111
(0.807) 		1
(1.00) 		0.0632
(0.739) 		0.235
(0.898) 		0.676
(1.00) 		0.712
(1.00) 		0.686
(1.00) 		0.52
(0.97) 		0.377
(0.953)
amp 1q21 3 55 (32%) 118 0.989
(1.00) 		0.195
(0.845) 		0.429
(0.969) 		0.448
(0.97) 		0.265
(0.912) 		0.591
(0.97) 		0.252
(0.912) 		0.219
(0.86) 		0.699
(1.00) 		0.593
(0.97) 		0.68
(1.00) 		0.67
(1.00) 		1
(1.00) 		0.21
(0.845)
amp 2q36 2 23 (13%) 150 0.861
(1.00) 		0.469
(0.97) 		0.654
(0.995) 		0.441
(0.969) 		0.324
(0.947) 		1
(1.00) 		0.177
(0.845) 		0.499
(0.97) 		0.55
(0.97) 		0.272
(0.912) 		0.212
(0.845) 		0.424
(0.969) 		0.258
(0.912) 		1
(1.00)
amp 3p12 2 11 (6%) 162 0.0263
(0.593) 		0.397
(0.969) 		1
(1.00) 		0.841
(1.00) 		1
(1.00) 		1
(1.00) 		0.00114
(0.336) 		0.545
(0.97) 		0.833
(1.00) 		0.249
(0.91) 		0.503
(0.97) 		1
(1.00)
amp 4p16 3 13 (8%) 160 0.185
(0.845) 		0.153
(0.845) 		0.474
(0.97) 		0.599
(0.972) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.00425
(0.593) 		0.325
(0.947) 		0.529
(0.97) 		0.87
(1.00) 		0.293
(0.912) 		0.203
(0.845)
amp 6p21 31 9 (5%) 164 0.734
(1.00) 		0.819
(1.00) 		0.285
(0.912) 		0.176
(0.845) 		0.211
(0.845) 		0.138
(0.838) 		1
(1.00) 		0.314
(0.932) 		0.625
(0.976) 		0.349
(0.947) 		0.434
(0.969) 		1
(1.00)
amp 7q22 1 54 (31%) 119 0.87
(1.00) 		0.266
(0.912) 		0.207
(0.845) 		0.596
(0.97) 		0.705
(1.00) 		0.301
(0.912) 		0.0992
(0.774) 		0.443
(0.969) 		0.212
(0.845) 		0.412
(0.969) 		0.0273
(0.593) 		0.299
(0.912) 		0.268
(0.912) 		1
(1.00)
amp 8p11 22 33 (19%) 140 0.462
(0.97) 		0.0672
(0.745) 		0.377
(0.953) 		0.567
(0.97) 		0.512
(0.97) 		1
(1.00) 		0.173
(0.845) 		0.776
(1.00) 		0.884
(1.00) 		0.666
(1.00) 		0.16
(0.845) 		0.859
(1.00) 		0.503
(0.97) 		0.468
(0.97)
amp 8p11 21 32 (18%) 141 0.97
(1.00) 		0.308
(0.927) 		0.732
(1.00) 		0.831
(1.00) 		0.822
(1.00) 		1
(1.00) 		0.115
(0.816) 		0.29
(0.912) 		0.907
(1.00) 		0.616
(0.975) 		0.287
(0.912) 		0.749
(1.00) 		0.493
(0.97) 		0.439
(0.969)
amp 8q24 21 69 (40%) 104 0.0873
(0.757) 		0.978
(1.00) 		0.751
(1.00) 		0.865
(1.00) 		0.375
(0.953) 		1
(1.00) 		0.353
(0.947) 		0.521
(0.97) 		0.414
(0.969) 		0.501
(0.97) 		0.373
(0.953) 		0.408
(0.969) 		0.0431
(0.678) 		0.561
(0.97)
amp 9p13 3 23 (13%) 150 0.878
(1.00) 		0.026
(0.593) 		0.778
(1.00) 		0.565
(0.97) 		1
(1.00) 		0.404
(0.969) 		0.37
(0.953) 		0.168
(0.845) 		0.508
(0.97) 		0.69
(1.00) 		0.925
(1.00) 		0.927
(1.00) 		1
(1.00) 		1
(1.00)
amp 12p13 33 37 (21%) 136 0.628
(0.977) 		0.935
(1.00) 		0.313
(0.931) 		0.144
(0.845) 		0.828
(1.00) 		1
(1.00) 		0.0951
(0.76) 		0.0233
(0.593) 		0.494
(0.97) 		0.71
(1.00) 		0.0161
(0.593) 		0.0526
(0.704) 		0.829
(1.00) 		1
(1.00)
amp 12p11 21 40 (23%) 133 0.692
(1.00) 		0.991
(1.00) 		0.138
(0.838) 		0.499
(0.97) 		1
(1.00) 		0.552
(0.97) 		0.0731
(0.745) 		0.13
(0.838) 		0.471
(0.97) 		0.695
(1.00) 		0.0117
(0.593) 		0.185
(0.845) 		1
(1.00) 		1
(1.00)
amp 12q15 28 (16%) 145 0.291
(0.912) 		0.377
(0.953) 		0.104
(0.803) 		0.277
(0.912) 		1
(1.00) 		1
(1.00) 		0.151
(0.845) 		0.0565
(0.712) 		0.176
(0.845) 		0.786
(1.00) 		0.0192
(0.593) 		0.137
(0.838) 		1
(1.00) 		0.439
(0.969)
amp 15q26 1 21 (12%) 152 0.309
(0.927) 		0.352
(0.947) 		0.272
(0.912) 		0.774
(1.00) 		0.285
(0.912) 		1
(1.00) 		0.819
(1.00) 		0.0956
(0.76) 		0.456
(0.97) 		0.767
(1.00) 		0.581
(0.97) 		0.164
(0.845) 		0.0338
(0.593) 		0.294
(0.912)
amp 17p11 2 14 (8%) 159 0.00881
(0.593) 		0.0833
(0.749) 		0.113
(0.807) 		0.0283
(0.593) 		0.486
(0.97) 		1
(1.00) 		0.783
(1.00) 		0.00553
(0.593) 		1
(1.00) 		0.843
(1.00) 		0.591
(0.97) 		1
(1.00)
amp 17q12 29 (17%) 144 0.175
(0.845) 		0.262
(0.912) 		0.261
(0.912) 		0.509
(0.97) 		0.633
(0.978) 		1
(1.00) 		0.838
(1.00) 		0.183
(0.845) 		0.204
(0.845) 		0.789
(1.00) 		0.222
(0.861) 		0.336
(0.947) 		0.622
(0.975) 		1
(1.00)
amp 18q11 2 50 (29%) 123 0.969
(1.00) 		0.944
(1.00) 		0.193
(0.845) 		0.212
(0.845) 		0.13
(0.838) 		0.128
(0.838) 		0.134
(0.838) 		0.207
(0.845) 		0.575
(0.97) 		0.962
(1.00) 		0.632
(0.978) 		0.802
(1.00) 		0.105
(0.807) 		0.571
(0.97)
amp 19p13 2 16 (9%) 157 0.052
(0.704) 		0.718
(1.00) 		0.189
(0.845) 		0.129
(0.838) 		0.359
(0.951) 		1
(1.00) 		0.298
(0.912) 		0.296
(0.912) 		0.857
(1.00) 		0.905
(1.00) 		0.447
(0.97) 		0.241
(0.899) 		1
(1.00) 		1
(1.00)
amp 19q13 2 41 (24%) 132 0.664
(1.00) 		0.0935
(0.757) 		0.83
(1.00) 		0.413
(0.969) 		0.41
(0.969) 		0.571
(0.97) 		0.0208
(0.593) 		0.491
(0.97) 		0.984
(1.00) 		0.215
(0.845) 		0.326
(0.947) 		0.0341
(0.593) 		0.593
(0.97) 		1
(1.00)
amp 20p11 23 38 (22%) 135 0.395
(0.969) 		0.561
(0.97) 		0.765
(1.00) 		0.214
(0.845) 		0.532
(0.97) 		1
(1.00) 		0.143
(0.845) 		0.0603
(0.719) 		0.969
(1.00) 		0.676
(1.00) 		0.302
(0.912) 		0.384
(0.965) 		1
(1.00) 		1
(1.00)
amp xp22 11 11 (6%) 162 0.0274
(0.593) 		0.509
(0.97) 		0.398
(0.969) 		0.419
(0.969) 		0.701
(1.00) 		1
(1.00) 		0.756
(1.00) 		0.0277
(0.593) 		0.833
(1.00) 		0.852
(1.00) 		0.501
(0.97) 		1
(1.00)
amp xq27 1 20 (12%) 153 0.0731
(0.745) 		0.248
(0.91) 		0.59
(0.97) 		0.296
(0.912) 		1
(1.00) 		1
(1.00) 		0.812
(1.00) 		0.027
(0.593) 		0.173
(0.845) 		0.567
(0.97) 		0.0507
(0.704) 		0.311
(0.93)
del 1p36 32 50 (29%) 123 0.956
(1.00) 		0.964
(1.00) 		0.257
(0.912) 		0.0813
(0.747) 		0.124
(0.838) 		1
(1.00) 		0.0297
(0.593) 		0.658
(0.997) 		0.387
(0.967) 		0.111
(0.807) 		0.755
(1.00) 		0.215
(0.845) 		0.36
(0.951) 		1
(1.00)
del 1p36 11 65 (38%) 108 0.358
(0.951) 		0.328
(0.947) 		0.193
(0.845) 		0.0745
(0.745) 		0.151
(0.845) 		1
(1.00) 		0.0115
(0.593) 		0.917
(1.00) 		0.167
(0.845) 		0.112
(0.807) 		0.419
(0.969) 		0.367
(0.953) 		0.0977
(0.769) 		1
(1.00)
del 2q14 3 9 (5%) 164 0.397
(0.969) 		0.335
(0.947) 		0.149
(0.845) 		0.539
(0.97) 		0.44
(0.969) 		1
(1.00) 		0.516
(0.97) 		0.0499
(0.704) 		0.281
(0.912) 		0.756
(1.00) 		0.193
(0.845) 		1
(1.00)
del 3p21 31 50 (29%) 123 0.824
(1.00) 		0.921
(1.00) 		0.908
(1.00) 		0.867
(1.00) 		0.706
(1.00) 		0.568
(0.97) 		0.0297
(0.593) 		0.756
(1.00) 		0.744
(1.00) 		0.589
(0.97) 		0.889
(1.00) 		0.5
(0.97) 		1
(1.00) 		1
(1.00)
del 4p15 31 27 (16%) 146 0.0794
(0.745) 		0.943
(1.00) 		0.872
(1.00) 		0.42
(0.969) 		1
(1.00) 		0.552
(0.97) 		0.0354
(0.601) 		0.348
(0.947) 		0.623
(0.975) 		0.431
(0.969) 		0.531
(0.97) 		0.508
(0.97) 		0.6
(0.972) 		0.424
(0.969)
del 4q22 1 25 (14%) 148 0.257
(0.912) 		0.603
(0.972) 		0.979
(1.00) 		0.686
(1.00) 		0.621
(0.975) 		1
(1.00) 		0.0289
(0.593) 		0.0147
(0.593) 		0.518
(0.97) 		0.155
(0.845) 		0.858
(1.00) 		0.594
(0.97) 		0.562
(0.97) 		0.0497
(0.704)
del 4q34 3 33 (19%) 140 0.453
(0.97) 		0.402
(0.969) 		0.584
(0.97) 		0.762
(1.00) 		0.827
(1.00) 		1
(1.00) 		0.0794
(0.745) 		0.498
(0.97) 		0.228
(0.873) 		0.702
(1.00) 		0.346
(0.947) 		0.895
(1.00) 		0.0907
(0.757) 		0.091
(0.757)
del 5q14 2 32 (18%) 141 0.0694
(0.745) 		0.278
(0.912) 		0.581
(0.97) 		0.532
(0.97) 		1
(1.00) 		1
(1.00) 		0.56
(0.97) 		0.057
(0.712) 		0.0494
(0.704) 		0.513
(0.97) 		0.377
(0.953) 		0.615
(0.975) 		0.109
(0.807) 		0.091
(0.757)
del 6p25 2 68 (39%) 105 0.436
(0.969) 		0.174
(0.845) 		0.328
(0.947) 		0.717
(1.00) 		0.375
(0.953) 		0.137
(0.838) 		0.161
(0.845) 		0.0308
(0.593) 		0.168
(0.845) 		0.348
(0.947) 		0.689
(1.00) 		0.291
(0.912) 		0.447
(0.97) 		1
(1.00)
del 6p22 2 65 (38%) 108 0.376
(0.953) 		0.222
(0.861) 		0.478
(0.97) 		0.645
(0.991) 		0.289
(0.912) 		0.151
(0.845) 		0.345
(0.947) 		0.0524
(0.704) 		0.151
(0.845) 		0.65
(0.995) 		0.647
(0.993) 		0.153
(0.845) 		0.446
(0.97) 		1
(1.00)
del 6q25 3 86 (50%) 87 0.11
(0.807) 		0.866
(1.00) 		0.438
(0.969) 		0.124
(0.838) 		1
(1.00) 		1
(1.00) 		0.0933
(0.757) 		0.759
(1.00) 		0.6
(0.972) 		0.9
(1.00) 		0.701
(1.00) 		0.585
(0.97) 		0.178
(0.845) 		0.606
(0.972)
del 7q36 1 12 (7%) 161 0.637
(0.981) 		0.189
(0.845) 		0.963
(1.00) 		0.505
(0.97) 		0.519
(0.97) 		1
(1.00) 		1
(1.00) 		0.561
(0.97) 		0.596
(0.97) 		0.202
(0.845) 		0.657
(0.997) 		0.272
(0.912) 		1
(1.00) 		1
(1.00)
del 8p23 2 55 (32%) 118 0.947
(1.00) 		0.463
(0.97) 		0.681
(1.00) 		0.176
(0.845) 		0.348
(0.947) 		1
(1.00) 		0.14
(0.845) 		0.711
(1.00) 		0.214
(0.845) 		0.9
(1.00) 		0.591
(0.97) 		0.208
(0.845) 		0.0246
(0.593) 		0.552
(0.97)
del 9p21 3 108 (62%) 65 0.0169
(0.593) 		0.898
(1.00) 		0.402
(0.969) 		0.631
(0.978) 		0.718
(1.00) 		1
(1.00) 		0.272
(0.912) 		0.0763
(0.745) 		0.747
(1.00) 		0.668
(1.00) 		0.706
(1.00) 		0.578
(0.97) 		0.273
(0.912) 		0.28
(0.912)
del 9q22 33 46 (27%) 127 0.608
(0.972) 		0.652
(0.995) 		0.164
(0.845) 		0.905
(1.00) 		1
(1.00) 		0.578
(0.97) 		0.73
(1.00) 		0.288
(0.912) 		0.378
(0.953) 		0.269
(0.912) 		0.929
(1.00) 		0.351
(0.947) 		0.867
(1.00) 		0.158
(0.845)
del 10p15 3 36 (21%) 137 0.297
(0.912) 		0.594
(0.97) 		0.145
(0.845) 		0.695
(1.00) 		0.394
(0.969) 		0.2
(0.845) 		1
(1.00) 		0.184
(0.845) 		0.592
(0.97) 		0.32
(0.947) 		0.801
(1.00) 		0.213
(0.845) 		0.328
(0.947) 		1
(1.00)
del 10q23 33 32 (18%) 141 0.554
(0.97) 		0.888
(1.00) 		0.174
(0.845) 		1
(1.00) 		0.0715
(0.745) 		1
(1.00) 		0.695
(1.00) 		0.169
(0.845) 		0.55
(0.97) 		0.341
(0.947) 		0.687
(1.00) 		0.201
(0.845) 		0.278
(0.912) 		0.439
(0.969)
del 11p15 4 27 (16%) 146 0.694
(1.00) 		0.521
(0.97) 		0.0856
(0.755) 		1
(1.00) 		0.0161
(0.593) 		1
(1.00) 		0.678
(1.00) 		1
(1.00) 		0.423
(0.969) 		0.24
(0.899) 		0.561
(0.97) 		0.0593
(0.719) 		0.207
(0.845) 		0.393
(0.969)
del 12p13 1 25 (14%) 148 0.623
(0.975) 		0.358
(0.951) 		0.849
(1.00) 		0.413
(0.969) 		1
(1.00) 		0.525
(0.97) 		0.388
(0.967) 		0.265
(0.912) 		0.109
(0.807) 		0.936
(1.00) 		0.0907
(0.757) 		0.993
(1.00) 		0.561
(0.97) 		1
(1.00)
del 12q12 22 (13%) 151 0.0789
(0.745) 		0.429
(0.969) 		0.774
(1.00) 		0.882
(1.00) 		1
(1.00) 		0.578
(0.97) 		0.652
(0.995) 		0.865
(1.00) 		0.366
(0.953) 		0.675
(1.00) 		0.909
(1.00) 		0.858
(1.00) 		1
(1.00) 		1
(1.00)
del 12q21 33 40 (23%) 133 0.222
(0.861) 		0.475
(0.97) 		0.976
(1.00) 		0.891
(1.00) 		1
(1.00) 		1
(1.00) 		0.476
(0.97) 		0.929
(1.00) 		0.529
(0.97) 		0.744
(1.00) 		0.86
(1.00) 		0.704
(1.00) 		0.0597
(0.719) 		0.55
(0.97)
del 12q24 33 39 (23%) 134 0.516
(0.97) 		0.62
(0.975) 		0.965
(1.00) 		0.72
(1.00) 		0.835
(1.00) 		0.568
(0.97) 		0.367
(0.953) 		0.93
(1.00) 		0.29
(0.912) 		0.956
(1.00) 		0.423
(0.969) 		0.608
(0.972) 		0.00101
(0.336) 		1
(1.00)
del 13q14 2 20 (12%) 153 0.406
(0.969) 		0.777
(1.00) 		0.545
(0.97) 		0.674
(1.00) 		0.285
(0.912) 		0.436
(0.969) 		0.812
(1.00) 		0.213
(0.845) 		0.256
(0.912) 		0.672
(1.00) 		0.214
(0.845) 		0.469
(0.97) 		1
(1.00) 		0.345
(0.947)
del 14q11 2 17 (10%) 156 0.919
(1.00) 		0.549
(0.97) 		0.227
(0.872) 		0.919
(1.00) 		0.136
(0.838) 		1
(1.00) 		0.802
(1.00) 		0.456
(0.97) 		0.183
(0.845) 		0.604
(0.972) 		0.78
(1.00) 		0.749
(1.00) 		0.0788
(0.745) 		1
(1.00)
del 15q15 1 32 (18%) 141 0.806
(1.00) 		0.0774
(0.745) 		0.321
(0.947) 		0.616
(0.975) 		0.501
(0.97) 		0.552
(0.97) 		0.238
(0.899) 		0.0735
(0.745) 		0.766
(1.00) 		0.789
(1.00) 		0.703
(1.00) 		0.497
(0.97) 		0.777
(1.00) 		0.424
(0.969)
del 16q23 1 16 (9%) 157 0.915
(1.00) 		0.735
(1.00) 		0.136
(0.838) 		0.491
(0.97) 		0.358
(0.951) 		0.299
(0.912) 		0.116
(0.816) 		0.0133
(0.593) 		0.302
(0.912) 		0.733
(1.00) 		0.122
(0.838) 		0.45
(0.97) 		0.365
(0.953) 		1
(1.00)
del 17p12 83 (48%) 90 0.0551
(0.712) 		0.813
(1.00) 		0.182
(0.845) 		0.236
(0.898) 		0.491
(0.97) 		1
(1.00) 		1
(1.00) 		0.072
(0.745) 		0.0573
(0.712) 		0.502
(0.97) 		0.0254
(0.593) 		0.867
(1.00) 		1
(1.00) 		1
(1.00)
del 17q22 46 (27%) 127 0.0495
(0.704) 		0.94
(1.00) 		0.524
(0.97) 		0.57
(0.97) 		1
(1.00) 		0.574
(0.97) 		0.73
(1.00) 		0.111
(0.807) 		0.0217
(0.593) 		0.56
(0.97) 		0.0262
(0.593) 		0.874
(1.00) 		0.508
(0.97) 		0.571
(0.97)
del 18p11 31 48 (28%) 125 0.568
(0.97) 		0.033
(0.593) 		0.903
(1.00) 		0.973
(1.00) 		0.698
(1.00) 		0.591
(0.97) 		0.612
(0.975) 		0.347
(0.947) 		0.869
(1.00) 		0.893
(1.00) 		0.966
(1.00) 		0.986
(1.00) 		1
(1.00) 		0.175
(0.845)
del 18q21 2 117 (68%) 56 0.0163
(0.593) 		0.0763
(0.745) 		0.0343
(0.593) 		0.0848
(0.755) 		0.574
(0.97) 		0.569
(0.97) 		0.0339
(0.593) 		0.02
(0.593) 		0.587
(0.97) 		0.653
(0.995) 		0.0378
(0.618) 		0.919
(1.00) 		0.554
(0.97) 		0.553
(0.97)
del 19p13 3 33 (19%) 140 0.198
(0.845) 		0.289
(0.912) 		0.353
(0.947) 		0.205
(0.845) 		0.125
(0.838) 		1
(1.00) 		0.561
(0.97) 		0.134
(0.838) 		0.348
(0.947) 		0.733
(1.00) 		0.343
(0.947) 		0.0156
(0.593) 		1
(1.00) 		0.468
(0.97)
del 19p13 2 25 (14%) 148 0.518
(0.97) 		0.438
(0.969) 		0.552
(0.97) 		0.0753
(0.745) 		0.0881
(0.757) 		1
(1.00) 		0.388
(0.967) 		0.0554
(0.712) 		0.53
(0.97) 		0.938
(1.00) 		0.442
(0.969) 		0.0153
(0.593) 		1
(1.00) 		0.377
(0.953)
del 19q13 33 22 (13%) 151 0.62
(0.975) 		0.0396
(0.634) 		0.699
(1.00) 		0.485
(0.97) 		0.199
(0.845) 		1
(1.00) 		0.0372
(0.618) 		0.207
(0.845) 		0.463
(0.97) 		0.011
(0.593) 		0.92
(1.00) 		0.0921
(0.757) 		0.0637
(0.739) 		1
(1.00)
del 21q11 2 57 (33%) 116 0.122
(0.838) 		0.285
(0.912) 		0.13
(0.838) 		0.00657
(0.593) 		0.00964
(0.593) 		0.633
(0.978) 		0.628
(0.977) 		0.154
(0.845) 		0.281
(0.912) 		0.297
(0.912) 		0.333
(0.947) 		0.00361
(0.593) 		0.742
(1.00) 		0.248
(0.91)
del 22q13 31 56 (32%) 117 0.532
(0.97) 		0.0448
(0.694) 		0.0276
(0.593) 		0.246
(0.91) 		0.457
(0.97) 		0.606
(0.972) 		0.193
(0.845) 		1
(1.00) 		0.0805
(0.747) 		0.261
(0.912) 		0.326
(0.947) 		0.616
(0.975) 		0.239
(0.899) 		0.551
(0.97)
del 22q13 32 58 (34%) 115 0.717
(1.00) 		0.0149
(0.593) 		0.186
(0.845) 		0.434
(0.969) 		0.582
(0.97) 		0.606
(0.972) 		0.335
(0.947) 		0.951
(1.00) 		0.0341
(0.593) 		0.434
(0.969) 		0.0831
(0.749) 		0.412
(0.969) 		0.247
(0.91) 		0.551
(0.97)
del xp21 1 27 (16%) 146 0.37
(0.953) 		0.9
(1.00) 		0.179
(0.845) 		0.472
(0.97) 		0.339
(0.947) 		1
(1.00) 		0.405
(0.969) 		0.578
(0.97) 		0.425
(0.969) 		0.191
(0.845) 		0.146
(0.845) 		0.124
(0.838) 		0.764
(1.00) 		0.409
(0.969)
del xq11 2 21 (12%) 152 0.572
(0.97) 		0.499
(0.97) 		0.278
(0.912) 		0.692
(1.00) 		0.42
(0.969) 		1
(1.00) 		0.159
(0.845) 		0.252
(0.912) 		0.0479
(0.704) 		0.0685
(0.745) 		0.44
(0.969) 		0.128
(0.838) 		0.478
(0.97) 		1
(1.00)
'amp_3q26.2' versus 'Time to Death'

P value = 2.41e-05 (logrank test), Q value = 0.021

Table S1.  Gene #6: 'amp_3q26.2' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 171 92 0.1 - 84.1 (14.2)
AMP PEAK 6(3Q26.2) MUTATED 30 22 0.1 - 24.3 (9.4)
AMP PEAK 6(3Q26.2) WILD-TYPE 141 70 0.2 - 84.1 (15.3)

Figure S1.  Get High-res Image Gene #6: 'amp_3q26.2' versus Clinical Feature #1: 'Time to Death'

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/PAAD-TP/15096458/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 focal cnvs = 63

  • 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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