Correlation between copy number variations of arm-level result and selected clinical features
Adrenocortical Carcinoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C1DF6QBQ
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/C1DF6QBQ
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 82 arm-level events and 12 clinical features across 90 patients, 12 significant findings detected with Q value < 0.25.

  • 2p gain cnv correlated to 'Time to Death'.

  • 10q gain cnv correlated to 'Time to Death',  'PATHOLOGIC_STAGE', and 'RESIDUAL_TUMOR'.

  • 11p gain cnv correlated to 'Time to Death'.

  • 11q gain cnv correlated to 'Time to Death'.

  • 4p loss cnv correlated to 'Time to Death'.

  • 4q loss cnv correlated to 'Time to Death'.

  • 16p loss cnv correlated to 'Time to Death'.

  • 17p loss cnv correlated to 'Time to Death'.

  • 19p loss cnv correlated to 'Time to Death'.

  • 20p loss cnv correlated to 'RESIDUAL_TUMOR'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 82 arm-level events and 12 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 12 significant findings detected.

Clinical
Features 		Time
to
Death 		YEARS
TO
BIRTH 		PATHOLOGIC
STAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		GENDER RADIATION
THERAPY 		HISTOLOGICAL
TYPE 		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 Fisher's exact test Fisher's exact test
10q gain 26 (29%) 64 0.00137
(0.15) 		0.266
(1.00) 		0.00179
(0.176) 		0.00557
(0.338) 		1
(1.00) 		1
(1.00) 		0.771
(1.00) 		0.515
(1.00) 		0.0011
(0.135) 		0.763
(1.00) 		1
(1.00) 		0.421
(1.00)
2p gain 13 (14%) 77 0.000374
(0.0735) 		0.818
(1.00) 		0.378
(1.00) 		0.143
(0.909) 		0.347
(1.00) 		0.205
(0.96) 		0.727
(1.00) 		1
(1.00) 		0.226
(0.977) 		0.235
(0.984) 		0.169
(0.949) 		0.587
(1.00)
11p gain 5 (6%) 85 0.0001
(0.028) 		0.364
(1.00) 		0.157
(0.925) 		0.043
(0.714) 		1
(1.00) 		0.656
(1.00) 		0.579
(1.00) 		1
(1.00) 		0.0103
(0.43) 		1
(1.00) 		0.569
(1.00)
11q gain 6 (7%) 84 5.25e-05
(0.0258) 		0.698
(1.00) 		0.12
(0.87) 		0.0624
(0.758) 		1
(1.00) 		0.66
(1.00) 		1
(1.00) 		1
(1.00) 		0.0635
(0.762) 		0.318
(1.00) 		1
(1.00) 		1
(1.00)
4p loss 10 (11%) 80 0.000114
(0.028) 		0.542
(1.00) 		0.0183
(0.516) 		0.00382
(0.289) 		1
(1.00) 		1
(1.00) 		0.0835
(0.857) 		1
(1.00) 		0.0388
(0.693) 		1
(1.00) 		1
(1.00) 		1
(1.00)
4q loss 11 (12%) 79 1.4e-05
(0.0138) 		0.805
(1.00) 		0.0225
(0.54) 		0.00619
(0.338) 		1
(1.00) 		0.742
(1.00) 		0.205
(0.96) 		1
(1.00) 		0.0114
(0.43) 		0.818
(1.00) 		1
(1.00) 		1
(1.00)
16p loss 6 (7%) 84 0.000658
(0.108) 		0.418
(1.00) 		0.117
(0.87) 		0.0509
(0.758) 		0.526
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.00809
(0.379) 		1
(1.00) 		1
(1.00) 		0.444
(1.00)
17p loss 32 (36%) 58 0.000962
(0.135) 		0.535
(1.00) 		0.0605
(0.758) 		0.14
(0.909) 		0.73
(1.00) 		0.246
(1.00) 		0.275
(1.00) 		1
(1.00) 		0.111
(0.87) 		0.747
(1.00) 		0.699
(1.00) 		0.409
(1.00)
19p loss 5 (6%) 85 0.00287
(0.236) 		0.603
(1.00) 		0.195
(0.952) 		0.287
(1.00) 		1
(1.00) 		1
(1.00) 		0.576
(1.00) 		1
(1.00) 		0.16
(0.927) 		1
(1.00) 		1
(1.00)
20p loss 9 (10%) 81 0.828
(1.00) 		0.595
(1.00) 		0.557
(1.00) 		0.747
(1.00) 		1
(1.00) 		0.156
(0.925) 		0.385
(1.00) 		1
(1.00) 		0.00203
(0.182) 		0.969
(1.00) 		0.278
(1.00) 		0.548
(1.00)
1p gain 4 (4%) 86 0.0866
(0.87) 		0.487
(1.00) 		1
(1.00) 		0.747
(1.00) 		1
(1.00) 		0.294
(1.00) 		0.576
(1.00) 		1
(1.00) 		0.301
(1.00) 		0.318
(1.00) 		0.144
(0.909) 		1
(1.00)
1q gain 8 (9%) 82 0.0407
(0.705) 		0.798
(1.00) 		0.733
(1.00) 		0.455
(1.00) 		0.589
(1.00) 		0.047
(0.745) 		1
(1.00) 		1
(1.00) 		0.51
(1.00) 		0.173
(0.949) 		0.245
(1.00) 		0.548
(1.00)
2q gain 12 (13%) 78 0.0106
(0.43) 		0.767
(1.00) 		0.154
(0.925) 		0.234
(0.984) 		1
(1.00) 		0.0516
(0.758) 		1
(1.00) 		1
(1.00) 		0.39
(1.00) 		0.235
(0.984) 		0.171
(0.949) 		0.645
(1.00)
3p gain 13 (14%) 77 0.263
(1.00) 		0.323
(1.00) 		0.582
(1.00) 		0.931
(1.00) 		1
(1.00) 		0.759
(1.00) 		0.0616
(0.758) 		0.0724
(0.819) 		0.77
(1.00) 		0.581
(1.00) 		1
(1.00) 		1
(1.00)
3q gain 15 (17%) 75 0.371
(1.00) 		0.423
(1.00) 		0.334
(1.00) 		0.756
(1.00) 		0.677
(1.00) 		1
(1.00) 		0.0337
(0.65) 		0.0958
(0.87) 		0.487
(1.00) 		0.581
(1.00) 		1
(1.00) 		1
(1.00)
4p gain 37 (41%) 53 0.224
(0.977) 		0.941
(1.00) 		0.791
(1.00) 		0.844
(1.00) 		1
(1.00) 		0.654
(1.00) 		0.592
(1.00) 		0.141
(0.909) 		0.206
(0.96) 		0.718
(1.00) 		1
(1.00) 		0.421
(1.00)
4q gain 33 (37%) 57 0.114
(0.87) 		0.97
(1.00) 		0.96
(1.00) 		0.93
(1.00) 		1
(1.00) 		0.495
(1.00) 		0.791
(1.00) 		0.409
(1.00) 		0.413
(1.00) 		0.567
(1.00) 		1
(1.00) 		0.669
(1.00)
5p gain 57 (63%) 33 0.451
(1.00) 		0.854
(1.00) 		0.693
(1.00) 		0.894
(1.00) 		1
(1.00) 		1
(1.00) 		0.272
(1.00) 		1
(1.00) 		0.559
(1.00) 		0.621
(1.00) 		1
(1.00) 		0.226
(0.977)
5q gain 53 (59%) 37 0.84
(1.00) 		0.62
(1.00) 		0.567
(1.00) 		0.797
(1.00) 		1
(1.00) 		1
(1.00) 		0.189
(0.949) 		0.786
(1.00) 		0.813
(1.00) 		0.485
(1.00) 		0.183
(0.949) 		0.115
(0.87)
6p gain 18 (20%) 72 0.66
(1.00) 		0.0275
(0.575) 		0.497
(1.00) 		0.255
(1.00) 		0.679
(1.00) 		0.588
(1.00) 		0.506
(1.00) 		1
(1.00) 		0.0257
(0.575) 		0.407
(1.00) 		0.0917
(0.87) 		0.0548
(0.758)
6q gain 16 (18%) 74 0.765
(1.00) 		0.2
(0.96) 		0.114
(0.87) 		0.175
(0.949) 		0.2
(0.96) 		0.399
(1.00) 		0.179
(0.949) 		0.634
(1.00) 		0.119
(0.87) 		0.127
(0.876) 		0.0582
(0.758) 		0.613
(1.00)
7p gain 48 (53%) 42 0.815
(1.00) 		0.51
(1.00) 		0.166
(0.949) 		0.233
(0.984) 		0.336
(1.00) 		1
(1.00) 		0.793
(1.00) 		0.621
(1.00) 		0.77
(1.00) 		0.361
(1.00) 		0.214
(0.963) 		0.435
(1.00)
7q gain 48 (53%) 42 0.512
(1.00) 		0.859
(1.00) 		0.108
(0.87) 		0.226
(0.977) 		0.336
(1.00) 		1
(1.00) 		0.431
(1.00) 		0.619
(1.00) 		0.772
(1.00) 		0.268
(1.00) 		0.216
(0.964) 		0.115
(0.87)
8p gain 32 (36%) 58 0.222
(0.977) 		0.508
(1.00) 		0.443
(1.00) 		0.637
(1.00) 		0.484
(1.00) 		1
(1.00) 		0.786
(1.00) 		0.542
(1.00) 		1
(1.00) 		1
(1.00) 		0.29
(1.00) 		0.421
(1.00)
8q gain 38 (42%) 52 0.649
(1.00) 		0.49
(1.00) 		0.344
(1.00) 		0.538
(1.00) 		0.51
(1.00) 		1
(1.00) 		0.594
(1.00) 		0.447
(1.00) 		0.798
(1.00) 		0.83
(1.00) 		0.344
(1.00) 		0.7
(1.00)
9p gain 20 (22%) 70 0.266
(1.00) 		0.716
(1.00) 		0.0601
(0.758) 		0.326
(1.00) 		0.00792
(0.379) 		0.791
(1.00) 		0.105
(0.87) 		0.251
(1.00) 		0.0714
(0.817) 		0.0118
(0.43) 		1
(1.00) 		0.374
(1.00)
9q gain 29 (32%) 61 0.0147
(0.468) 		0.663
(1.00) 		0.0369
(0.685) 		0.0892
(0.87) 		0.013
(0.441) 		0.477
(1.00) 		0.402
(1.00) 		0.389
(1.00) 		0.0508
(0.758) 		0.0177
(0.516) 		1
(1.00) 		0.421
(1.00)
10p gain 25 (28%) 65 0.011
(0.43) 		0.397
(1.00) 		0.00616
(0.338) 		0.0147
(0.468) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.691
(1.00) 		0.0105
(0.43) 		0.763
(1.00) 		1
(1.00) 		0.421
(1.00)
12p gain 64 (71%) 26 0.894
(1.00) 		0.287
(1.00) 		0.701
(1.00) 		0.607
(1.00) 		1
(1.00) 		0.464
(1.00) 		0.38
(1.00) 		1
(1.00) 		0.638
(1.00) 		0.703
(1.00) 		0.648
(1.00) 		0.0898
(0.87)
12q gain 64 (71%) 26 0.917
(1.00) 		0.415
(1.00) 		0.703
(1.00) 		0.653
(1.00) 		0.718
(1.00) 		0.464
(1.00) 		0.38
(1.00) 		1
(1.00) 		0.656
(1.00) 		0.703
(1.00) 		0.0832
(0.857) 		0.0898
(0.87)
13q gain 6 (7%) 84 0.839
(1.00) 		0.651
(1.00) 		0.735
(1.00) 		0.722
(1.00) 		0.526
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.503
(1.00) 		0.633
(1.00) 		1
(1.00) 		0.548
(1.00)
14q gain 21 (23%) 69 0.13
(0.876) 		0.426
(1.00) 		0.181
(0.949) 		0.313
(1.00) 		0.241
(0.998) 		0.606
(1.00) 		0.0606
(0.758) 		0.669
(1.00) 		0.731
(1.00) 		0.149
(0.917) 		1
(1.00) 		0.374
(1.00)
15q gain 11 (12%) 79 0.779
(1.00) 		0.46
(1.00) 		0.794
(1.00) 		0.711
(1.00) 		1
(1.00) 		1
(1.00) 		0.425
(1.00) 		1
(1.00) 		1
(1.00) 		0.917
(1.00) 		1
(1.00) 		1
(1.00)
16p gain 49 (54%) 41 0.336
(1.00) 		0.576
(1.00) 		0.595
(1.00) 		0.283
(1.00) 		1
(1.00) 		0.187
(0.949) 		0.793
(1.00) 		1
(1.00) 		0.975
(1.00) 		0.394
(1.00) 		0.725
(1.00) 		0.439
(1.00)
16q gain 47 (52%) 43 0.35
(1.00) 		0.929
(1.00) 		0.834
(1.00) 		0.616
(1.00) 		1
(1.00) 		0.269
(1.00) 		0.112
(0.87) 		1
(1.00) 		0.931
(1.00) 		0.394
(1.00) 		0.115
(0.87) 		0.699
(1.00)
17p gain 5 (6%) 85 0.291
(1.00) 		0.622
(1.00) 		0.159
(0.927) 		0.108
(0.87) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.0681
(0.798) 		0.501
(1.00) 		0.318
(1.00) 		0.147
(0.915) 		0.444
(1.00)
17q gain 7 (8%) 83 0.124
(0.873) 		0.488
(1.00) 		0.692
(1.00) 		0.471
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.0206
(0.519) 		0.581
(1.00) 		1
(1.00) 		0.548
(1.00)
18p gain 6 (7%) 84 0.129
(0.876) 		0.452
(1.00) 		0.342
(1.00) 		0.332
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.206
(0.96) 		0.214
(0.963) 		1
(1.00)
18q gain 5 (6%) 85 0.309
(1.00) 		0.833
(1.00) 		0.83
(1.00) 		0.288
(1.00) 		1
(1.00) 		0.656
(1.00) 		0.579
(1.00) 		1
(1.00) 		0.113
(0.87) 		0.178
(0.949) 		0.569
(1.00)
19p gain 56 (62%) 34 0.289
(1.00) 		0.119
(0.87) 		0.178
(0.949) 		0.203
(0.96) 		0.737
(1.00) 		0.821
(1.00) 		0.105
(0.87) 		1
(1.00) 		0.77
(1.00) 		0.552
(1.00) 		1
(1.00) 		0.124
(0.873)
19q gain 52 (58%) 38 0.318
(1.00) 		0.0203
(0.519) 		0.202
(0.96) 		0.326
(1.00) 		0.182
(0.949) 		0.378
(1.00) 		0.108
(0.87) 		0.79
(1.00) 		0.251
(1.00) 		0.321
(1.00) 		1
(1.00) 		0.124
(0.873)
20p gain 46 (51%) 44 0.141
(0.909) 		0.495
(1.00) 		0.339
(1.00) 		0.799
(1.00) 		1
(1.00) 		0.188
(0.949) 		0.3
(1.00) 		0.615
(1.00) 		0.466
(1.00) 		0.917
(1.00) 		0.495
(1.00) 		1
(1.00)
20q gain 49 (54%) 41 0.542
(1.00) 		0.964
(1.00) 		0.318
(1.00) 		0.86
(1.00) 		0.336
(1.00) 		0.187
(0.949) 		0.431
(1.00) 		0.622
(1.00) 		0.248
(1.00) 		0.396
(1.00) 		0.214
(0.963) 		0.71
(1.00)
21q gain 31 (34%) 59 0.68
(1.00) 		0.154
(0.925) 		0.936
(1.00) 		0.941
(1.00) 		0.0836
(0.857) 		0.818
(1.00) 		0.4
(1.00) 		0.4
(1.00) 		0.972
(1.00) 		0.0907
(0.87) 		0.272
(1.00) 		0.443
(1.00)
22q gain 3 (3%) 87 0.131
(0.876) 		0.208
(0.961) 		1
(1.00) 		1
(1.00) 		0.307
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.625
(1.00) 		1
(1.00) 		1
(1.00)
xp gain 42 (47%) 48 0.617
(1.00) 		0.916
(1.00) 		0.866
(1.00) 		0.87
(1.00) 		1
(1.00) 		0.828
(1.00) 		0.434
(1.00) 		0.619
(1.00) 		0.169
(0.949) 		0.57
(1.00) 		0.347
(1.00) 		0.115
(0.87)
xq gain 41 (46%) 49 0.472
(1.00) 		0.77
(1.00) 		0.546
(1.00) 		0.914
(1.00) 		0.327
(1.00) 		0.824
(1.00) 		0.289
(1.00) 		0.62
(1.00) 		0.155
(0.925) 		0.405
(1.00) 		0.342
(1.00) 		0.435
(1.00)
1p loss 29 (32%) 61 0.902
(1.00) 		0.866
(1.00) 		0.957
(1.00) 		0.952
(1.00) 		1
(1.00) 		1
(1.00) 		0.26
(1.00) 		0.255
(1.00) 		1
(1.00) 		0.292
(1.00) 		1
(1.00) 		1
(1.00)
1q loss 20 (22%) 70 0.799
(1.00) 		0.317
(1.00) 		0.564
(1.00) 		0.744
(1.00) 		0.445
(1.00) 		0.599
(1.00) 		0.208
(0.961) 		0.0691
(0.8) 		0.436
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
2p loss 17 (19%) 73 0.0334
(0.65) 		0.442
(1.00) 		1
(1.00) 		0.719
(1.00) 		1
(1.00) 		0.576
(1.00) 		0.734
(1.00) 		0.0435
(0.714) 		0.898
(1.00) 		0.581
(1.00) 		1
(1.00) 		1
(1.00)
2q loss 15 (17%) 75 0.0609
(0.758) 		0.689
(1.00) 		0.618
(1.00) 		0.757
(1.00) 		1
(1.00) 		0.767
(1.00) 		0.475
(1.00) 		0.0305
(0.624) 		0.837
(1.00) 		0.753
(1.00) 		1
(1.00) 		1
(1.00)
3p loss 20 (22%) 70 0.115
(0.87) 		0.614
(1.00) 		0.0925
(0.87) 		0.343
(1.00) 		1
(1.00) 		0.293
(1.00) 		0.745
(1.00) 		1
(1.00) 		0.027
(0.575) 		0.77
(1.00) 		1
(1.00) 		1
(1.00)
3q loss 20 (22%) 70 0.191
(0.949) 		0.907
(1.00) 		0.178
(0.949) 		0.559
(1.00) 		1
(1.00) 		0.599
(1.00) 		1
(1.00) 		1
(1.00) 		0.172
(0.949) 		0.77
(1.00) 		0.251
(1.00) 		0.277
(1.00)
5p loss 8 (9%) 82 0.127
(0.876) 		0.676
(1.00) 		0.189
(0.949) 		0.148
(0.917) 		1
(1.00) 		1
(1.00) 		0.668
(1.00) 		1
(1.00) 		0.195
(0.952) 		0.235
(0.984) 		1
(1.00) 		0.548
(1.00)
5q loss 7 (8%) 83 0.551
(1.00) 		0.342
(1.00) 		0.0762
(0.842) 		0.142
(0.909) 		0.584
(1.00) 		0.228
(0.978) 		0.152
(0.922) 		1
(1.00) 		0.135
(0.889) 		1
(1.00) 		1
(1.00)
6p loss 19 (21%) 71 0.11
(0.87) 		0.35
(1.00) 		0.0822
(0.857) 		0.147
(0.915) 		0.445
(1.00) 		1
(1.00) 		1
(1.00) 		0.0607
(0.758) 		0.246
(1.00) 		0.5
(1.00) 		1
(1.00) 		0.571
(1.00)
6q loss 22 (24%) 68 0.0259
(0.575) 		0.254
(1.00) 		0.00701
(0.363) 		0.0187
(0.516) 		0.706
(1.00) 		0.453
(1.00) 		1
(1.00) 		0.0922
(0.87) 		0.0408
(0.705) 		0.671
(1.00) 		1
(1.00) 		1
(1.00)
7p loss 5 (6%) 85 0.109
(0.87) 		0.718
(1.00) 		0.336
(1.00) 		0.288
(1.00) 		1
(1.00) 		0.0461
(0.744) 		0.576
(1.00) 		1
(1.00) 		0.172
(0.949) 		1
(1.00) 		1
(1.00)
7q loss 6 (7%) 84 0.0173
(0.516) 		0.61
(1.00) 		0.0381
(0.693) 		0.0194
(0.516) 		1
(1.00) 		0.411
(1.00) 		1
(1.00) 		1
(1.00) 		0.26
(1.00) 		1
(1.00) 		1
(1.00)
8p loss 16 (18%) 74 0.821
(1.00) 		0.768
(1.00) 		0.668
(1.00) 		0.97
(1.00) 		0.365
(1.00) 		1
(1.00) 		0.725
(1.00) 		1
(1.00) 		0.0262
(0.575) 		0.854
(1.00) 		1
(1.00) 		1
(1.00)
8q loss 12 (13%) 78 0.892
(1.00) 		0.639
(1.00) 		0.579
(1.00) 		1
(1.00) 		0.107
(0.87) 		0.534
(1.00) 		1
(1.00) 		1
(1.00) 		0.0808
(0.857) 		0.25
(1.00) 		1
(1.00) 		1
(1.00)
9p loss 20 (22%) 70 0.174
(0.949) 		0.506
(1.00) 		0.845
(1.00) 		0.619
(1.00) 		0.683
(1.00) 		0.599
(1.00) 		0.061
(0.758) 		0.668
(1.00) 		0.822
(1.00) 		0.193
(0.952) 		1
(1.00) 		0.645
(1.00)
9q loss 11 (12%) 79 0.857
(1.00) 		0.427
(1.00) 		0.213
(0.963) 		0.425
(1.00) 		0.596
(1.00) 		1
(1.00) 		0.425
(1.00) 		1
(1.00) 		0.317
(1.00) 		0.235
(0.984) 		1
(1.00) 		0.569
(1.00)
10p loss 12 (13%) 78 0.311
(1.00) 		0.934
(1.00) 		0.183
(0.949) 		1
(1.00) 		0.134
(0.889) 		1
(1.00) 		1
(1.00) 		0.0617
(0.758) 		0.529
(1.00) 		0.116
(0.87) 		1
(1.00) 		0.444
(1.00)
10q loss 10 (11%) 80 0.383
(1.00) 		0.298
(1.00) 		0.307
(1.00) 		0.712
(1.00) 		0.317
(1.00) 		1
(1.00) 		1
(1.00) 		0.0432
(0.714) 		0.478
(1.00) 		0.152
(0.922) 		1
(1.00) 		1
(1.00)
11p loss 24 (27%) 66 0.473
(1.00) 		0.722
(1.00) 		0.131
(0.876) 		0.604
(1.00) 		0.706
(1.00) 		0.455
(1.00) 		1
(1.00) 		0.116
(0.87) 		0.476
(1.00) 		0.671
(1.00) 		1
(1.00) 		1
(1.00)
11q loss 23 (26%) 67 0.158
(0.925) 		0.563
(1.00) 		0.0271
(0.575) 		0.163
(0.94) 		1
(1.00) 		0.317
(1.00) 		1
(1.00) 		0.103
(0.87) 		0.687
(1.00) 		0.854
(1.00) 		1
(1.00) 		0.569
(1.00)
12p loss 5 (6%) 85 0.181
(0.949) 		0.241
(0.998) 		0.334
(1.00) 		0.287
(1.00) 		1
(1.00) 		0.335
(1.00) 		1
(1.00) 		1
(1.00) 		0.0583
(0.758) 		0.318
(1.00) 		1
(1.00) 		1
(1.00)
12q loss 4 (4%) 86 0.0594
(0.758) 		0.463
(1.00) 		0.334
(1.00) 		0.286
(1.00) 		1
(1.00) 		0.606
(1.00) 		1
(1.00) 		1
(1.00) 		0.0587
(0.758) 		0.318
(1.00) 		1
(1.00) 		1
(1.00)
13q loss 39 (43%) 51 0.114
(0.87) 		0.536
(1.00) 		0.485
(1.00) 		0.921
(1.00) 		0.51
(1.00) 		0.51
(1.00) 		1
(1.00) 		0.205
(0.96) 		0.866
(1.00) 		0.606
(1.00) 		0.507
(1.00) 		1
(1.00)
14q loss 18 (20%) 72 0.72
(1.00) 		0.793
(1.00) 		0.834
(1.00) 		0.78
(1.00) 		0.68
(1.00) 		0.782
(1.00) 		1
(1.00) 		0.0534
(0.758) 		0.531
(1.00) 		0.265
(1.00) 		0.218
(0.964) 		0.129
(0.876)
15q loss 21 (23%) 69 0.679
(1.00) 		0.519
(1.00) 		0.647
(1.00) 		0.705
(1.00) 		1
(1.00) 		0.606
(1.00) 		0.218
(0.964) 		0.0795
(0.857) 		0.96
(1.00) 		0.333
(1.00) 		1
(1.00) 		0.664
(1.00)
16q loss 5 (6%) 85 0.0193
(0.516) 		0.214
(0.963) 		0.247
(1.00) 		0.14
(0.909) 		0.461
(1.00) 		1
(1.00) 		0.275
(1.00) 		1
(1.00) 		0.114
(0.87) 		1
(1.00) 		0.444
(1.00)
17q loss 24 (27%) 66 0.0129
(0.441) 		0.964
(1.00) 		0.19
(0.949) 		0.36
(1.00) 		0.706
(1.00) 		0.00587
(0.338) 		0.377
(1.00) 		0.687
(1.00) 		0.217
(0.964) 		0.583
(1.00) 		1
(1.00) 		0.664
(1.00)
18p loss 37 (41%) 53 0.599
(1.00) 		0.892
(1.00) 		0.21
(0.963) 		0.494
(1.00) 		1
(1.00) 		0.37
(1.00) 		0.295
(1.00) 		0.59
(1.00) 		0.182
(0.949) 		0.816
(1.00) 		0.291
(1.00) 		1
(1.00)
18q loss 35 (39%) 55 0.934
(1.00) 		0.747
(1.00) 		0.274
(1.00) 		0.521
(1.00) 		1
(1.00) 		0.11
(0.87) 		0.584
(1.00) 		0.426
(1.00) 		0.647
(1.00) 		0.816
(1.00) 		0.274
(1.00) 		1
(1.00)
19q loss 4 (4%) 86 0.0746
(0.834) 		0.124
(0.873) 		0.876
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.576
(1.00) 		1
(1.00) 		0.735
(1.00) 		0.318
(1.00) 		1
(1.00) 		1
(1.00)
20q loss 3 (3%) 87 0.408
(1.00) 		0.582
(1.00) 		0.703
(1.00) 		0.525
(1.00) 		1
(1.00) 		0.549
(1.00) 		1
(1.00) 		1
(1.00) 		0.0367
(0.685) 		1
(1.00) 		0.321
(1.00)
21q loss 15 (17%) 75 0.0214
(0.527) 		0.468
(1.00) 		0.669
(1.00) 		0.418
(1.00) 		1
(1.00) 		0.565
(1.00) 		0.502
(1.00) 		0.031
(0.624) 		0.52
(1.00) 		0.475
(1.00) 		1
(1.00) 		1
(1.00)
22q loss 48 (53%) 42 0.0059
(0.338) 		0.236
(0.984) 		0.189
(0.949) 		0.0806
(0.857) 		1
(1.00) 		0.374
(1.00) 		1
(1.00) 		1
(1.00) 		0.755
(1.00) 		0.51
(1.00) 		1
(1.00) 		0.117
(0.87)
xp loss 16 (18%) 74 0.752
(1.00) 		0.0502
(0.758) 		0.861
(1.00) 		0.866
(1.00) 		0.677
(1.00) 		0.778
(1.00) 		0.29
(1.00) 		0.631
(1.00) 		1
(1.00) 		0.974
(1.00) 		1
(1.00) 		0.571
(1.00)
xq loss 15 (17%) 75 0.725
(1.00) 		0.12
(0.87) 		0.7
(1.00) 		0.551
(1.00) 		0.194
(0.952) 		1
(1.00) 		0.0647
(0.767) 		0.607
(1.00) 		1
(1.00) 		0.116
(0.87) 		1
(1.00) 		0.571
(1.00)
'2p gain' versus 'Time to Death'

P value = 0.000374 (logrank test), Q value = 0.074

Table S1.  Gene #3: '2p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 90 33 0.0 - 153.6 (38.9)
2P GAIN MUTATED 13 10 0.0 - 91.3 (16.4)
2P GAIN WILD-TYPE 77 23 4.1 - 153.6 (39.5)

Figure S1.  Get High-res Image Gene #3: '2p gain' versus Clinical Feature #1: 'Time to Death'

'10q gain' versus 'Time to Death'

P value = 0.00137 (logrank test), Q value = 0.15

Table S2.  Gene #20: '10q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 90 33 0.0 - 153.6 (38.9)
10Q GAIN MUTATED 26 15 0.0 - 91.3 (32.0)
10Q GAIN WILD-TYPE 64 18 4.1 - 153.6 (43.9)

Figure S2.  Get High-res Image Gene #20: '10q gain' versus Clinical Feature #1: 'Time to Death'

'10q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00179 (Fisher's exact test), Q value = 0.18

Table S3.  Gene #20: '10q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 9 43 18 18
10Q GAIN MUTATED 0 8 6 11
10Q GAIN WILD-TYPE 9 35 12 7

Figure S3.  Get High-res Image Gene #20: '10q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'10q gain' versus 'RESIDUAL_TUMOR'

P value = 0.0011 (Fisher's exact test), Q value = 0.14

Table S4.  Gene #20: '10q gain' versus Clinical Feature #9: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 63 7 12 5
10Q GAIN MUTATED 12 2 9 1
10Q GAIN WILD-TYPE 51 5 3 4

Figure S4.  Get High-res Image Gene #20: '10q gain' versus Clinical Feature #9: 'RESIDUAL_TUMOR'

'11p gain' versus 'Time to Death'

P value = 1e-04 (logrank test), Q value = 0.028

Table S5.  Gene #21: '11p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 90 33 0.0 - 153.6 (38.9)
11P GAIN MUTATED 5 5 0.0 - 60.9 (14.3)
11P GAIN WILD-TYPE 85 28 4.1 - 153.6 (39.2)

Figure S5.  Get High-res Image Gene #21: '11p gain' versus Clinical Feature #1: 'Time to Death'

'11q gain' versus 'Time to Death'

P value = 5.25e-05 (logrank test), Q value = 0.026

Table S6.  Gene #22: '11q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 90 33 0.0 - 153.6 (38.9)
11Q GAIN MUTATED 6 6 12.6 - 60.9 (16.2)
11Q GAIN WILD-TYPE 84 27 0.0 - 153.6 (39.4)

Figure S6.  Get High-res Image Gene #22: '11q gain' versus Clinical Feature #1: 'Time to Death'

'4p loss' versus 'Time to Death'

P value = 0.000114 (logrank test), Q value = 0.028

Table S7.  Gene #48: '4p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 90 33 0.0 - 153.6 (38.9)
4P LOSS MUTATED 10 7 4.1 - 46.5 (18.1)
4P LOSS WILD-TYPE 80 26 0.0 - 153.6 (41.0)

Figure S7.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #1: 'Time to Death'

'4q loss' versus 'Time to Death'

P value = 1.4e-05 (logrank test), Q value = 0.014

Table S8.  Gene #49: '4q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 90 33 0.0 - 153.6 (38.9)
4Q LOSS MUTATED 11 8 4.1 - 46.5 (18.1)
4Q LOSS WILD-TYPE 79 25 0.0 - 153.6 (42.5)

Figure S8.  Get High-res Image Gene #49: '4q loss' versus Clinical Feature #1: 'Time to Death'

'16p loss' versus 'Time to Death'

P value = 0.000658 (logrank test), Q value = 0.11

Table S9.  Gene #69: '16p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 90 33 0.0 - 153.6 (38.9)
16P LOSS MUTATED 6 5 12.6 - 39.4 (18.1)
16P LOSS WILD-TYPE 84 28 0.0 - 153.6 (39.5)

Figure S9.  Get High-res Image Gene #69: '16p loss' versus Clinical Feature #1: 'Time to Death'

'17p loss' versus 'Time to Death'

P value = 0.000962 (logrank test), Q value = 0.14

Table S10.  Gene #71: '17p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 90 33 0.0 - 153.6 (38.9)
17P LOSS MUTATED 32 18 4.1 - 91.3 (31.5)
17P LOSS WILD-TYPE 58 15 0.0 - 153.6 (43.9)

Figure S10.  Get High-res Image Gene #71: '17p loss' versus Clinical Feature #1: 'Time to Death'

'19p loss' versus 'Time to Death'

P value = 0.00287 (logrank test), Q value = 0.24

Table S11.  Gene #75: '19p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 90 33 0.0 - 153.6 (38.9)
19P LOSS MUTATED 5 4 12.6 - 44.5 (18.1)
19P LOSS WILD-TYPE 85 29 0.0 - 153.6 (39.4)

Figure S11.  Get High-res Image Gene #75: '19p loss' versus Clinical Feature #1: 'Time to Death'

'20p loss' versus 'RESIDUAL_TUMOR'

P value = 0.00203 (Fisher's exact test), Q value = 0.18

Table S12.  Gene #77: '20p loss' versus Clinical Feature #9: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 63 7 12 5
20P LOSS MUTATED 3 4 0 0
20P LOSS WILD-TYPE 60 3 12 5

Figure S12.  Get High-res Image Gene #77: '20p loss' versus Clinical Feature #9: 'RESIDUAL_TUMOR'

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/ACC-TP/19778621/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/ACC-TP/19775006/ACC-TP.merged_data.txt

  • Number of patients = 90

  • Number of significantly arm-level cnvs = 82

  • Number of selected clinical features = 12

  • 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)
Copyright © 2015 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle