Correlation between copy number variation genes (focal events) and selected clinical features
Pancreatic Adenocarcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1348JTS
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 variation genes (focal events) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1348JTS
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 56 focal events and 15 clinical features across 184 patients, 2 significant findings detected with Q value < 0.25.

  • amp_3p12.2 cnv correlated to 'GENDER'.

  • 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 56 focal 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
amp 3p12 2 12 (7%) 172 0.275
(0.909) 		0.512
(0.982) 		0.787
(1.00) 		0.849
(1.00) 		0.741
(1.00) 		0.417
(0.962) 		0.000591
(0.248) 		0.189
(0.882) 		1
(1.00) 		1
(1.00) 		0.454
(0.976) 		0.495
(0.982) 		1
(1.00)
amp 3q26 2 32 (17%) 152 0.000129
(0.108) 		0.794
(1.00) 		0.644
(0.997) 		0.547
(0.982) 		0.518
(0.982) 		0.237
(0.882) 		0.117
(0.84) 		0.11
(0.821) 		1
(1.00) 		0.943
(1.00) 		0.0638
(0.821) 		0.0653
(0.821) 		0.0286
(0.782) 		0.6
(0.982) 		1
(1.00)
amp 1p34 2 13 (7%) 171 0.48
(0.982) 		0.00524
(0.732) 		0.26
(0.904) 		0.407
(0.962) 		1
(1.00) 		0.0467
(0.798) 		0.389
(0.958) 		0.518
(0.982) 		0.00867
(0.732) 		0.269
(0.909) 		0.2
(0.882) 		1
(1.00) 		0.312
(0.928)
amp 1p12 27 (15%) 157 0.521
(0.982) 		0.222
(0.882) 		0.207
(0.882) 		0.461
(0.978) 		1
(1.00) 		0.0311
(0.782) 		1
(1.00) 		0.623
(0.992) 		0.11
(0.821) 		0.222
(0.882) 		0.659
(0.997) 		0.561
(0.982) 		0.526
(0.982) 		0.454
(0.976) 		0.559
(0.982)
amp 1q21 3 62 (34%) 122 0.926
(1.00) 		0.135
(0.846) 		0.215
(0.882) 		0.48
(0.982) 		0.218
(0.882) 		0.335
(0.928) 		0.273
(0.909) 		0.461
(0.978) 		0.395
(0.958) 		0.765
(1.00) 		0.636
(0.997) 		0.729
(1.00) 		0.692
(1.00) 		0.305
(0.928) 		0.166
(0.857)
amp 2q36 2 26 (14%) 158 0.74
(1.00) 		0.442
(0.971) 		0.548
(0.982) 		0.649
(0.997) 		0.472
(0.982) 		1
(1.00) 		0.138
(0.848) 		0.331
(0.928) 		0.782
(1.00) 		0.519
(0.982) 		0.277
(0.909) 		0.188
(0.882) 		0.398
(0.958) 		0.218
(0.882) 		1
(1.00)
amp 4p16 3 15 (8%) 169 0.357
(0.935) 		0.354
(0.933) 		0.606
(0.982) 		0.432
(0.97) 		0.758
(1.00) 		1
(1.00) 		1
(1.00) 		0.76
(1.00) 		0.00966
(0.732) 		0.325
(0.928) 		0.0665
(0.821) 		0.998
(1.00) 		0.0804
(0.821) 		0.312
(0.928)
amp 6p21 31 12 (7%) 172 0.313
(0.928) 		0.68
(1.00) 		0.0906
(0.821) 		0.166
(0.857) 		0.0754
(0.821) 		0.0341
(0.782) 		1
(1.00) 		1
(1.00) 		0.269
(0.909) 		0.758
(1.00) 		0.11
(0.821) 		0.345
(0.929) 		0.312
(0.928)
amp 7q22 1 56 (30%) 128 0.926
(1.00) 		0.328
(0.928) 		0.154
(0.857) 		0.56
(0.982) 		0.586
(0.982) 		0.129
(0.844) 		0.108
(0.821) 		0.448
(0.975) 		0.399
(0.958) 		0.239
(0.883) 		0.388
(0.958) 		0.0723
(0.821) 		0.387
(0.958) 		0.71
(1.00) 		1
(1.00)
amp 8p11 22 34 (18%) 150 0.468
(0.982) 		0.106
(0.821) 		0.508
(0.982) 		0.472
(0.982) 		0.83
(1.00) 		1
(1.00) 		0.127
(0.844) 		0.183
(0.874) 		0.708
(1.00) 		0.737
(1.00) 		0.653
(0.997) 		0.16
(0.857) 		0.761
(1.00) 		0.467
(0.982) 		1
(1.00)
amp 8p11 21 34 (18%) 150 0.968
(1.00) 		0.427
(0.965) 		0.841
(1.00) 		0.887
(1.00) 		1
(1.00) 		0.581
(0.982) 		0.127
(0.844) 		0.265
(0.909) 		0.205
(0.882) 		0.698
(1.00) 		0.601
(0.982) 		0.403
(0.96) 		0.847
(1.00) 		0.767
(1.00) 		1
(1.00)
amp 8q24 21 74 (40%) 110 0.105
(0.821) 		0.79
(1.00) 		0.897
(1.00) 		0.982
(1.00) 		0.396
(0.958) 		1
(1.00) 		0.227
(0.882) 		0.373
(0.958) 		0.543
(0.982) 		0.258
(0.904) 		0.485
(0.982) 		0.482
(0.982) 		0.367
(0.952) 		0.0754
(0.821) 		0.386
(0.958)
amp 9p13 3 24 (13%) 160 0.672
(0.998) 		0.0345
(0.782) 		0.759
(1.00) 		0.53
(0.982) 		0.805
(1.00) 		0.487
(0.982) 		0.273
(0.909) 		0.599
(0.982) 		0.191
(0.882) 		0.503
(0.982) 		0.696
(1.00) 		0.871
(1.00) 		0.874
(1.00) 		0.5
(0.982) 		0.52
(0.982)
amp 12p13 33 39 (21%) 145 0.845
(1.00) 		0.976
(1.00) 		0.388
(0.958) 		0.315
(0.928) 		0.836
(1.00) 		0.58
(0.982) 		0.0476
(0.798) 		0.142
(0.857) 		0.0168
(0.732) 		0.557
(0.982) 		0.653
(0.997) 		0.0192
(0.732) 		0.0573
(0.805) 		1
(1.00) 		0.584
(0.982)
amp 12p11 21 43 (23%) 141 0.911
(1.00) 		0.992
(1.00) 		0.26
(0.904) 		0.914
(1.00) 		0.689
(1.00) 		0.215
(0.882) 		0.0795
(0.821) 		0.413
(0.962) 		0.12
(0.84) 		0.526
(0.982) 		0.736
(1.00) 		0.0123
(0.732) 		0.23
(0.882) 		1
(1.00) 		0.584
(0.982)
amp 12q15 29 (16%) 155 0.556
(0.982) 		0.268
(0.909) 		0.247
(0.894) 		0.554
(0.982) 		0.811
(1.00) 		1
(1.00) 		0.108
(0.821) 		0.158
(0.857) 		0.108
(0.821) 		0.198
(0.882) 		0.75
(1.00) 		0.0163
(0.732) 		0.0839
(0.821) 		1
(1.00) 		1
(1.00)
amp 15q26 1 22 (12%) 162 0.495
(0.982) 		0.415
(0.962) 		0.22
(0.882) 		0.546
(0.982) 		0.196
(0.882) 		1
(1.00) 		0.654
(0.997) 		0.597
(0.982) 		0.0986
(0.821) 		0.49
(0.982) 		0.755
(1.00) 		0.615
(0.988) 		0.164
(0.857) 		0.15
(0.857) 		0.435
(0.97)
amp 17p11 2 15 (8%) 169 0.012
(0.732) 		0.127
(0.844) 		0.169
(0.857) 		0.133
(0.846) 		0.32
(0.928) 		1
(1.00) 		1
(1.00) 		0.76
(1.00) 		0.0109
(0.732) 		0.649
(0.997) 		0.859
(1.00) 		0.595
(0.982) 		1
(1.00)
amp 17q12 31 (17%) 153 0.179
(0.872) 		0.445
(0.975) 		0.259
(0.904) 		0.839
(1.00) 		0.648
(0.997) 		0.417
(0.962) 		0.697
(1.00) 		0.254
(0.902) 		0.126
(0.844) 		0.232
(0.882) 		0.769
(1.00) 		0.326
(0.928) 		0.422
(0.963) 		0.6
(0.982) 		1
(1.00)
amp 18q11 2 56 (30%) 128 0.844
(1.00) 		0.515
(0.982) 		0.0893
(0.821) 		0.25
(0.896) 		0.28
(0.909) 		0.0585
(0.805) 		0.199
(0.882) 		0.849
(1.00) 		0.165
(0.857) 		0.654
(0.997) 		0.926
(1.00) 		0.672
(0.998) 		0.78
(1.00) 		0.0965
(0.821) 		0.329
(0.928)
amp 19q13 2 47 (26%) 137 0.477
(0.982) 		0.0887
(0.821) 		0.949
(1.00) 		0.462
(0.978) 		0.701
(1.00) 		1
(1.00) 		0.0174
(0.732) 		0.843
(1.00) 		0.573
(0.982) 		0.984
(1.00) 		0.222
(0.882) 		0.451
(0.976) 		0.0717
(0.821) 		0.316
(0.928) 		1
(1.00)
amp 20p11 23 38 (21%) 146 0.571
(0.982) 		0.52
(0.982) 		0.79
(1.00) 		0.289
(0.922) 		0.683
(1.00) 		1
(1.00) 		0.146
(0.857) 		0.831
(1.00) 		0.0941
(0.821) 		0.99
(1.00) 		0.659
(0.997) 		0.244
(0.894) 		0.414
(0.962) 		0.211
(0.882) 		0.583
(0.982)
amp xq28 20 (11%) 164 0.108
(0.821) 		0.226
(0.882) 		0.607
(0.982) 		0.331
(0.928) 		0.279
(0.909) 		0.379
(0.958) 		0.476
(0.982) 		1
(1.00) 		0.0344
(0.782) 		0.635
(0.997) 		1
(1.00) 		0.153
(0.857) 		0.687
(1.00) 		0.457
(0.978)
del 1p36 11 68 (37%) 116 0.413
(0.962) 		0.265
(0.909) 		0.18
(0.873) 		0.0781
(0.821) 		0.231
(0.882) 		0.656
(0.997) 		0.0216
(0.732) 		0.476
(0.982) 		0.919
(1.00) 		0.212
(0.882) 		0.129
(0.844) 		0.144
(0.857) 		0.485
(0.982) 		0.577
(0.982) 		0.652
(0.997)
del 2q14 3 9 (5%) 175 0.237
(0.882) 		0.344
(0.928) 		0.16
(0.857) 		0.504
(0.982) 		0.688
(1.00) 		1
(1.00) 		0.516
(0.982) 		0.698
(1.00) 		0.0494
(0.798) 		0.285
(0.919) 		0.772
(1.00) 		0.621
(0.992) 		1
(1.00)
del 3p21 31 51 (28%) 133 0.421
(0.963) 		0.9
(1.00) 		0.836
(1.00) 		0.881
(1.00) 		1
(1.00) 		0.583
(0.982) 		0.0493
(0.798) 		0.337
(0.928) 		0.76
(1.00) 		0.813
(1.00) 		0.565
(0.982) 		0.936
(1.00) 		0.425
(0.963) 		0.913
(1.00) 		1
(1.00)
del 4q22 1 27 (15%) 157 0.403
(0.96) 		0.75
(1.00) 		0.847
(1.00) 		0.822
(1.00) 		0.35
(0.929) 		1
(1.00) 		0.0364
(0.782) 		1
(1.00) 		0.0512
(0.803) 		0.535
(0.982) 		0.146
(0.857) 		0.959
(1.00) 		0.41
(0.962) 		0.484
(0.982) 		0.134
(0.846)
del 4q34 3 35 (19%) 149 0.628
(0.997) 		0.52
(0.982) 		0.513
(0.982) 		0.839
(1.00) 		1
(1.00) 		0.579
(0.982) 		0.0894
(0.821) 		0.657
(0.997) 		0.607
(0.982) 		0.247
(0.894) 		0.689
(1.00) 		0.865
(1.00) 		0.875
(1.00) 		0.204
(0.882) 		0.229
(0.882)
del 5q14 2 35 (19%) 149 0.28
(0.909) 		0.399
(0.958) 		0.714
(1.00) 		0.634
(0.997) 		0.836
(1.00) 		0.581
(0.982) 		0.708
(1.00) 		0.376
(0.958) 		0.0919
(0.821) 		0.0591
(0.805) 		0.497
(0.982) 		0.774
(1.00) 		0.596
(0.982) 		0.323
(0.928) 		0.0484
(0.798)
del 6p25 2 74 (40%) 110 0.599
(0.982) 		0.156
(0.857) 		0.29
(0.922) 		0.835
(1.00) 		0.313
(0.928) 		0.0752
(0.821) 		0.131
(0.846) 		0.375
(0.958) 		0.105
(0.821) 		0.1
(0.821) 		0.393
(0.958) 		0.639
(0.997) 		0.232
(0.882) 		0.798
(1.00) 		1
(1.00)
del 6p22 2 70 (38%) 114 0.594
(0.982) 		0.149
(0.857) 		0.493
(0.982) 		0.671
(0.998) 		0.391
(0.958) 		0.152
(0.857) 		0.173
(0.857) 		0.858
(1.00) 		0.127
(0.844) 		0.088
(0.821) 		0.711
(1.00) 		0.794
(1.00) 		0.137
(0.846) 		0.927
(1.00) 		1
(1.00)
del 6q25 3 91 (49%) 93 0.12
(0.84) 		0.815
(1.00) 		0.397
(0.958) 		0.237
(0.882) 		1
(1.00) 		1
(1.00) 		0.0395
(0.782) 		1
(1.00) 		0.526
(0.982) 		0.423
(0.963) 		0.982
(1.00) 		0.895
(1.00) 		0.47
(0.982) 		0.413
(0.962) 		0.668
(0.998)
del 7q31 1 15 (8%) 169 0.833
(1.00) 		0.534
(0.982) 		0.761
(1.00) 		0.792
(1.00) 		0.764
(1.00) 		0.339
(0.928) 		0.592
(0.982) 		0.744
(1.00) 		0.109
(0.821) 		0.781
(1.00) 		0.809
(1.00) 		0.422
(0.963) 		0.338
(0.928)
del 7q36 1 15 (8%) 169 0.745
(1.00) 		0.319
(0.928) 		0.581
(0.982) 		0.43
(0.969) 		1
(1.00) 		0.298
(0.928) 		0.79
(1.00) 		1
(1.00) 		0.805
(1.00) 		0.584
(0.982) 		0.204
(0.882) 		0.78
(1.00) 		0.749
(1.00) 		1
(1.00) 		0.363
(0.945)
del 8p21 3 62 (34%) 122 0.878
(1.00) 		0.0526
(0.803) 		0.882
(1.00) 		0.308
(0.928) 		0.599
(0.982) 		0.656
(0.997) 		0.273
(0.909) 		0.58
(0.982) 		0.526
(0.982) 		0.118
(0.84) 		0.793
(1.00) 		0.537
(0.982) 		0.313
(0.928) 		0.217
(0.882) 		0.665
(0.997)
del 9p21 3 116 (63%) 68 0.0155
(0.732) 		0.782
(1.00) 		0.226
(0.882) 		0.646
(0.997) 		0.493
(0.982) 		1
(1.00) 		0.22
(0.882) 		0.592
(0.982) 		0.0363
(0.782) 		0.561
(0.982) 		0.606
(0.982) 		0.709
(1.00) 		0.54
(0.982) 		0.235
(0.882) 		0.648
(0.997)
del 10p15 3 41 (22%) 143 0.385
(0.958) 		0.487
(0.982) 		0.215
(0.882) 		0.56
(0.982) 		0.314
(0.928) 		0.307
(0.928) 		1
(1.00) 		0.683
(1.00) 		0.288
(0.922) 		0.331
(0.928) 		0.339
(0.928) 		0.537
(0.982) 		0.182
(0.874) 		0.0831
(0.821) 		1
(1.00)
del 10q23 33 35 (19%) 149 0.841
(1.00) 		0.775
(1.00) 		0.171
(0.857) 		1
(1.00) 		0.202
(0.882) 		0.331
(0.928) 		0.573
(0.982) 		0.659
(0.997) 		0.169
(0.857) 		0.534
(0.982) 		0.352
(0.93) 		0.604
(0.982) 		0.438
(0.97) 		0.62
(0.992) 		0.229
(0.882)
del 11p15 4 29 (16%) 155 0.35
(0.929) 		0.392
(0.958) 		0.182
(0.874) 		1
(1.00) 		0.037
(0.782) 		0.585
(0.982) 		0.424
(0.963) 		0.48
(0.982) 		1
(1.00) 		0.441
(0.971) 		0.23
(0.882) 		0.49
(0.982) 		0.0596
(0.805) 		0.497
(0.982) 		0.173
(0.857)
del 12p13 1 29 (16%) 155 0.981
(1.00) 		0.549
(0.982) 		0.856
(1.00) 		0.567
(0.982) 		0.821
(1.00) 		1
(1.00) 		0.424
(0.963) 		0.0884
(0.821) 		0.277
(0.909) 		0.0423
(0.782) 		0.938
(1.00) 		0.0426
(0.782) 		0.7
(1.00) 		0.072
(0.821) 		1
(1.00)
del 12q24 33 43 (23%) 141 0.956
(1.00) 		0.788
(1.00) 		0.894
(1.00) 		0.343
(0.928) 		0.56
(0.982) 		1
(1.00) 		0.294
(0.928) 		0.681
(1.00) 		1
(1.00) 		0.153
(0.857) 		0.915
(1.00) 		0.393
(0.958) 		0.784
(1.00) 		0.00351
(0.732) 		0.591
(0.982)
del 14q11 2 20 (11%) 164 0.692
(1.00) 		0.779
(1.00) 		0.355
(0.933) 		0.864
(1.00) 		0.177
(0.868) 		0.417
(0.962) 		0.813
(1.00) 		1
(1.00) 		0.439
(0.971) 		0.201
(0.882) 		0.613
(0.988) 		0.671
(0.998) 		0.788
(1.00) 		0.0539
(0.805) 		1
(1.00)
del 15q15 1 36 (20%) 148 0.697
(1.00) 		0.1
(0.821) 		0.478
(0.982) 		0.606
(0.982) 		0.529
(0.982) 		1
(1.00) 		0.136
(0.846) 		0.663
(0.997) 		0.077
(0.821) 		0.813
(1.00) 		0.772
(1.00) 		0.659
(0.997) 		0.685
(1.00) 		0.276
(0.909) 		0.201
(0.882)
del 16q23 1 19 (10%) 165 0.335
(0.928) 		0.922
(1.00) 		0.159
(0.857) 		0.435
(0.97) 		0.783
(1.00) 		0.417
(0.962) 		0.0933
(0.821) 		1
(1.00) 		0.0156
(0.732) 		0.32
(0.928) 		0.722
(1.00) 		0.15
(0.857) 		0.553
(0.982) 		0.151
(0.857) 		0.363
(0.945)
del 17p12 89 (48%) 95 0.0288
(0.782) 		0.678
(1.00) 		0.248
(0.894) 		0.401
(0.96) 		0.621
(0.992) 		0.656
(0.997) 		0.768
(1.00) 		0.729
(1.00) 		0.048
(0.798) 		0.0875
(0.821) 		0.53
(0.982) 		0.103
(0.821) 		0.926
(1.00) 		1
(1.00) 		1
(1.00)
del 17q22 49 (27%) 135 0.0218
(0.732) 		0.973
(1.00) 		0.75
(1.00) 		0.901
(1.00) 		1
(1.00) 		0.615
(0.988) 		0.867
(1.00) 		0.69
(1.00) 		0.0613
(0.805) 		0.0284
(0.782) 		0.542
(0.982) 		0.0203
(0.732) 		0.956
(1.00) 		0.573
(0.982) 		1
(1.00)
del 18p11 31 54 (29%) 130 0.976
(1.00) 		0.0217
(0.732) 		0.813
(1.00) 		0.951
(1.00) 		0.856
(1.00) 		0.343
(0.928) 		0.516
(0.982) 		0.7
(1.00) 		0.448
(0.975) 		0.817
(1.00) 		0.895
(1.00) 		0.978
(1.00) 		0.856
(1.00) 		0.434
(0.97) 		0.13
(0.844)
del 18q21 2 126 (68%) 58 0.0183
(0.732) 		0.0321
(0.782) 		0.0266
(0.782) 		0.126
(0.844) 		0.59
(0.982) 		0.323
(0.928) 		0.038
(0.782) 		0.46
(0.978) 		0.0169
(0.732) 		0.754
(1.00) 		0.608
(0.982) 		0.0839
(0.821) 		0.975
(1.00) 		0.23
(0.882) 		0.654
(0.997)
del 19p13 3 36 (20%) 148 0.564
(0.982) 		0.38
(0.958) 		0.35
(0.929) 		0.371
(0.957) 		0.298
(0.928) 		0.307
(0.928) 		0.458
(0.978) 		1
(1.00) 		0.193
(0.882) 		0.384
(0.958) 		0.78
(1.00) 		0.698
(1.00) 		0.0586
(0.805) 		0.716
(1.00) 		0.258
(0.904)
del 19p13 2 28 (15%) 156 0.891
(1.00) 		0.56
(0.982) 		0.84
(1.00) 		0.234
(0.882) 		0.254
(0.902) 		1
(1.00) 		0.309
(0.928) 		1
(1.00) 		0.11
(0.821) 		0.584
(0.982) 		0.878
(1.00) 		0.889
(1.00) 		0.0699
(0.821) 		1
(1.00) 		0.173
(0.857)
del 19q13 33 22 (12%) 162 0.553
(0.982) 		0.0422
(0.782) 		0.669
(0.998) 		0.512
(0.982) 		0.196
(0.882) 		1
(1.00) 		0.038
(0.782) 		0.599
(0.982) 		0.168
(0.857) 		0.454
(0.976) 		0.0116
(0.732) 		0.944
(1.00) 		0.0844
(0.821) 		0.599
(0.982) 		1
(1.00)
del 21q11 2 62 (34%) 122 0.34
(0.928) 		0.223
(0.882) 		0.135
(0.846) 		0.0103
(0.732) 		0.0137
(0.732) 		0.398
(0.958) 		0.638
(0.997) 		0.71
(1.00) 		0.222
(0.882) 		0.333
(0.928) 		0.311
(0.928) 		0.193
(0.882) 		0.0073
(0.732) 		0.923
(1.00) 		0.333
(0.928)
del 22q13 31 60 (33%) 124 0.437
(0.97) 		0.0697
(0.821) 		0.039
(0.782) 		0.285
(0.919) 		0.724
(1.00) 		0.343
(0.928) 		0.117
(0.84) 		0.852
(1.00) 		1
(1.00) 		0.112
(0.825) 		0.279
(0.909) 		0.369
(0.953) 		0.892
(1.00) 		0.664
(0.997) 		1
(1.00)
del 22q13 32 61 (33%) 123 0.387
(0.958) 		0.0295
(0.782) 		0.0856
(0.821) 		0.24
(0.883) 		1
(1.00) 		0.343
(0.928) 		0.161
(0.857) 		0.851
(1.00) 		1
(1.00) 		0.052
(0.803) 		0.454
(0.976) 		0.152
(0.857) 		0.653
(0.997) 		0.664
(0.997) 		0.661
(0.997)
del xp21 1 28 (15%) 156 0.221
(0.882) 		0.648
(0.997) 		0.162
(0.857) 		0.544
(0.982) 		0.254
(0.902) 		1
(1.00) 		0.309
(0.928) 		0.347
(0.929) 		0.327
(0.928) 		0.476
(0.982) 		0.173
(0.857) 		0.0994
(0.821) 		0.118
(0.84) 		0.753
(1.00) 		0.578
(0.982)
del xq11 2 23 (12%) 161 0.245
(0.894) 		0.731
(1.00) 		0.214
(0.882) 		0.831
(1.00) 		0.446
(0.975) 		1
(1.00) 		0.0718
(0.821) 		0.603
(0.982) 		0.0428
(0.782) 		0.0587
(0.805) 		0.0604
(0.805) 		0.269
(0.909) 		0.154
(0.857) 		0.348
(0.929) 		1
(1.00)
'amp_3p12.2' versus 'GENDER'

P value = 0.000591 (Fisher's exact test), Q value = 0.25

Table S1.  Gene #5: 'amp_3p12.2' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 83 101
AMP PEAK 5(3P12.2) MUTATED 0 12
AMP PEAK 5(3P12.2) WILD-TYPE 83 89

Figure S1.  Get High-res Image Gene #5: 'amp_3p12.2' versus Clinical Feature #7: 'GENDER'

'amp_3q26.2' versus 'Time to Death'

P value = 0.000129 (logrank test), Q value = 0.11

Table S2.  Gene #6: 'amp_3q26.2' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 183 100 0.1 - 90.1 (15.3)
AMP PEAK 6(3Q26.2) MUTATED 32 24 0.1 - 31.9 (9.6)
AMP PEAK 6(3Q26.2) WILD-TYPE 151 76 0.2 - 90.1 (15.8)

Figure S2.  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/22533736/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 focal cnvs = 56

  • Number of selected clinical features = 15

  • 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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