Correlation between copy number variations of arm-level result and selected clinical features
Rectum Adenocarcinoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C1V1242G
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/C1V1242G
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 12 clinical features across 165 patients, no significant finding detected with Q value < 0.25.

  • No arm-level cnvs related to clinical features.

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 12 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, no significant finding 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 		RESIDUAL
TUMOR 		NUMBER
OF
LYMPH
NODES 		RACE
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 Fisher's exact test Wilcoxon-test Fisher's exact test
1p gain 12 (7%) 153 0.0775
(0.67) 		0.564
(1.00) 		0.154
(0.805) 		0.0285
(0.531) 		0.442
(0.974) 		1
(1.00) 		0.774
(1.00) 		0.677
(1.00) 		0.0483
(0.568) 		0.22
(0.863) 		0.601
(1.00) 		1
(1.00)
1q gain 34 (21%) 131 0.746
(1.00) 		0.501
(0.978) 		0.529
(0.988) 		0.00488
(0.492) 		0.282
(0.884) 		1
(1.00) 		0.441
(0.974) 		0.129
(0.733) 		0.298
(0.884) 		0.573
(1.00) 		0.096
(0.695) 		0.484
(0.978)
2p gain 41 (25%) 124 0.761
(1.00) 		0.78
(1.00) 		0.505
(0.978) 		0.377
(0.974) 		0.216
(0.863) 		0.442
(0.974) 		0.0311
(0.531) 		0.272
(0.884) 		0.0222
(0.531) 		0.103
(0.7) 		0.869
(1.00) 		0.109
(0.7)
2q gain 43 (26%) 122 0.983
(1.00) 		0.964
(1.00) 		0.401
(0.974) 		0.26
(0.884) 		0.142
(0.782) 		0.609
(1.00) 		0.0332
(0.531) 		0.159
(0.812) 		0.0206
(0.531) 		0.147
(0.793) 		0.546
(0.996) 		0.0114
(0.492)
3p gain 27 (16%) 138 0.19
(0.843) 		0.819
(1.00) 		0.194
(0.857) 		0.834
(1.00) 		0.394
(0.974) 		0.224
(0.864) 		0.533
(0.989) 		0.504
(0.978) 		0.698
(1.00) 		0.886
(1.00) 		0.209
(0.863) 		1
(1.00)
3q gain 34 (21%) 131 0.422
(0.974) 		0.992
(1.00) 		0.294
(0.884) 		0.687
(1.00) 		0.491
(0.978) 		0.265
(0.884) 		0.441
(0.974) 		0.536
(0.989) 		0.302
(0.891) 		0.721
(1.00) 		0.29
(0.884) 		0.703
(1.00)
4p gain 9 (5%) 156 0.715
(1.00) 		0.914
(1.00) 		0.215
(0.863) 		0.65
(1.00) 		0.245
(0.883) 		1
(1.00) 		0.18
(0.841) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.0445
(0.563) 		1
(1.00)
4q gain 5 (3%) 160 0.89
(1.00) 		0.857
(1.00) 		0.902
(1.00) 		1
(1.00) 		0.709
(1.00) 		0.587
(1.00) 		0.0626
(0.653) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.439
(0.974)
5p gain 36 (22%) 129 0.927
(1.00) 		0.699
(1.00) 		0.756
(1.00) 		0.157
(0.812) 		0.713
(1.00) 		0.597
(1.00) 		0.092
(0.679) 		0.0338
(0.532) 		0.0412
(0.563) 		0.4
(0.974) 		0.532
(0.989) 		0.238
(0.88)
5q gain 24 (15%) 141 0.682
(1.00) 		0.936
(1.00) 		0.216
(0.863) 		0.582
(1.00) 		0.284
(0.884) 		0.756
(1.00) 		0.386
(0.974) 		0.144
(0.785) 		0.22
(0.863) 		0.539
(0.991) 		0.211
(0.863) 		0.333
(0.932)
6p gain 41 (25%) 124 0.265
(0.884) 		0.774
(1.00) 		0.224
(0.864) 		0.281
(0.884) 		0.0241
(0.531) 		0.0328
(0.531) 		0.588
(1.00) 		0.237
(0.877) 		0.187
(0.843) 		0.442
(0.974) 		0.0285
(0.531) 		0.0439
(0.563)
6q gain 36 (22%) 129 0.456
(0.975) 		0.917
(1.00) 		0.0497
(0.569) 		0.295
(0.884) 		0.0529
(0.587) 		0.0111
(0.492) 		0.576
(1.00) 		0.217
(0.863) 		0.0734
(0.658) 		0.257
(0.884) 		0.0709
(0.658) 		0.0329
(0.531)
7p gain 102 (62%) 63 0.614
(1.00) 		0.628
(1.00) 		0.0247
(0.531) 		0.434
(0.974) 		0.153
(0.805) 		0.65
(1.00) 		0.63
(1.00) 		1
(1.00) 		0.00466
(0.492) 		0.382
(0.974) 		0.0454
(0.563) 		0.769
(1.00)
7q gain 85 (52%) 80 0.853
(1.00) 		0.504
(0.978) 		0.00464
(0.492) 		0.546
(0.996) 		0.0664
(0.658) 		0.265
(0.884) 		0.534
(0.989) 		0.619
(1.00) 		0.00748
(0.492) 		0.172
(0.827) 		0.085
(0.679) 		0.219
(0.863)
8p gain 42 (25%) 123 0.408
(0.974) 		0.786
(1.00) 		0.167
(0.819) 		0.208
(0.863) 		0.699
(1.00) 		0.318
(0.915) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.15
(0.802) 		0.521
(0.987) 		1
(1.00)
8q gain 89 (54%) 76 0.211
(0.863) 		0.702
(1.00) 		0.0124
(0.492) 		0.116
(0.724) 		0.111
(0.705) 		0.126
(0.733) 		1
(1.00) 		0.457
(0.975) 		0.0896
(0.679) 		0.0828
(0.679) 		0.189
(0.843) 		0.521
(0.987)
9p gain 42 (25%) 123 0.481
(0.978) 		0.338
(0.938) 		0.401
(0.974) 		0.841
(1.00) 		0.72
(1.00) 		0.617
(1.00) 		1
(1.00) 		0.776
(1.00) 		0.322
(0.915) 		0.462
(0.975) 		0.898
(1.00) 		0.728
(1.00)
9q gain 33 (20%) 132 0.255
(0.884) 		0.199
(0.863) 		0.0373
(0.551) 		0.935
(1.00) 		0.932
(1.00) 		0.785
(1.00) 		0.439
(0.974) 		0.761
(1.00) 		0.298
(0.884) 		0.859
(1.00) 		0.889
(1.00) 		0.683
(1.00)
10p gain 13 (8%) 152 0.76
(1.00) 		0.88
(1.00) 		0.888
(1.00) 		0.422
(0.974) 		0.932
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.603
(1.00) 		1
(1.00) 		0.575
(1.00) 		0.452
(0.975)
10q gain 7 (4%) 158 0.463
(0.975) 		0.51
(0.981) 		0.7
(1.00) 		0.679
(1.00) 		0.874
(1.00) 		1
(1.00) 		0.25
(0.884) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.981
(1.00) 		0.288
(0.884)
11p gain 32 (19%) 133 0.606
(1.00) 		0.326
(0.917) 		0.852
(1.00) 		0.631
(1.00) 		0.458
(0.975) 		1
(1.00) 		0.845
(1.00) 		0.526
(0.988) 		0.0724
(0.658) 		1
(1.00) 		0.587
(1.00) 		0.0276
(0.531)
11q gain 26 (16%) 139 0.426
(0.974) 		0.13
(0.733) 		0.824
(1.00) 		0.442
(0.974) 		0.258
(0.884) 		0.375
(0.974) 		1
(1.00) 		1
(1.00) 		0.129
(0.733) 		0.792
(1.00) 		0.297
(0.884) 		0.0118
(0.492)
12p gain 33 (20%) 132 0.622
(1.00) 		0.421
(0.974) 		0.758
(1.00) 		0.438
(0.974) 		0.389
(0.974) 		0.572
(1.00) 		0.699
(1.00) 		0.235
(0.877) 		0.298
(0.884) 		0.398
(0.974) 		0.503
(0.978) 		0.164
(0.819)
12q gain 24 (15%) 141 0.145
(0.785) 		0.21
(0.863) 		0.875
(1.00) 		0.707
(1.00) 		0.559
(1.00) 		1
(1.00) 		0.507
(0.978) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.265
(0.884) 		0.647
(1.00)
13q gain 113 (68%) 52 0.793
(1.00) 		0.67
(1.00) 		0.29
(0.884) 		0.323
(0.915) 		0.0331
(0.531) 		1
(1.00) 		0.506
(0.978) 		0.29
(0.884) 		0.000593
(0.458) 		0.954
(1.00) 		0.0199
(0.531) 		0.0995
(0.7)
14q gain 8 (5%) 157 0.269
(0.884) 		0.894
(1.00) 		0.699
(1.00) 		1
(1.00) 		0.392
(0.974) 		1
(1.00) 		0.472
(0.978) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.642
(1.00) 		1
(1.00)
15q gain 3 (2%) 162 0.764
(1.00) 		0.922
(1.00) 		0.0773
(0.67) 		0.05
(0.569) 		0.171
(0.827) 		1
(1.00) 		0.0956
(0.695) 		1
(1.00) 		0.227
(0.864) 		1
(1.00) 		0.218
(0.863)
16p gain 41 (25%) 124 0.169
(0.825) 		0.777
(1.00) 		0.137
(0.764) 		0.787
(1.00) 		0.323
(0.915) 		1
(1.00) 		1
(1.00) 		0.244
(0.883) 		0.0222
(0.531) 		0.391
(0.974) 		0.294
(0.884) 		0.4
(0.974)
16q gain 41 (25%) 124 0.537
(0.989) 		0.853
(1.00) 		0.488
(0.978) 		0.934
(1.00) 		0.16
(0.812) 		0.297
(0.884) 		0.857
(1.00) 		0.392
(0.974) 		0.0222
(0.531) 		0.626
(1.00) 		0.215
(0.863) 		0.0962
(0.695)
17p gain 8 (5%) 157 0.367
(0.974) 		0.544
(0.996) 		0.617
(1.00) 		0.0408
(0.563) 		0.705
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.503
(0.978) 		1
(1.00) 		0.859
(1.00) 		1
(1.00)
17q gain 32 (19%) 133 0.268
(0.884) 		0.581
(1.00) 		0.925
(1.00) 		0.949
(1.00) 		0.606
(1.00) 		0.397
(0.974) 		0.556
(0.998) 		0.759
(1.00) 		0.469
(0.978) 		0.462
(0.975) 		0.748
(1.00) 		0.693
(1.00)
18p gain 8 (5%) 157 0.455
(0.975) 		0.425
(0.974) 		0.0354
(0.54) 		0.374
(0.974) 		0.495
(0.978) 		1
(1.00) 		0.727
(1.00) 		0.269
(0.884) 		0.131
(0.733) 		0.149
(0.799) 		0.104
(0.7) 		0.0661
(0.658)
18q gain 6 (4%) 159 0.00682
(0.492) 		0.391
(0.974) 		0.0234
(0.531) 		0.164
(0.819) 		0.0832
(0.679) 		0.506
(0.978) 		0.219
(0.863) 		0.199
(0.863) 		0.406
(0.974) 		0.0485
(0.568) 		0.00409
(0.492) 		0.0677
(0.658)
19p gain 33 (20%) 132 0.66
(1.00) 		0.441
(0.974) 		0.831
(1.00) 		0.266
(0.884) 		1
(1.00) 		0.292
(0.884) 		0.559
(1.00) 		0.744
(1.00) 		0.0718
(0.658) 		0.496
(0.978) 		0.788
(1.00) 		0.184
(0.841)
19q gain 32 (19%) 133 0.206
(0.863) 		0.491
(0.978) 		0.939
(1.00) 		0.181
(0.841) 		1
(1.00) 		0.277
(0.884) 		0.694
(1.00) 		0.733
(1.00) 		0.0724
(0.658) 		0.249
(0.884) 		0.639
(1.00) 		0.0914
(0.679)
20p gain 109 (66%) 56 0.409
(0.974) 		0.183
(0.841) 		0.00966
(0.492) 		0.777
(1.00) 		0.335
(0.933) 		0.643
(1.00) 		0.1
(0.7) 		1
(1.00) 		0.0328
(0.531) 		0.298
(0.884) 		0.335
(0.933) 		0.414
(0.974)
20q gain 145 (88%) 20 0.357
(0.964) 		0.14
(0.776) 		0.105
(0.7) 		0.565
(1.00) 		0.0296
(0.531) 		0.312
(0.908) 		0.812
(1.00) 		0.733
(1.00) 		0.000953
(0.458) 		0.182
(0.841) 		0.108
(0.7) 		0.1
(0.7)
21q gain 10 (6%) 155 0.688
(1.00) 		0.482
(0.978) 		0.546
(0.996) 		0.744
(1.00) 		0.905
(1.00) 		0.637
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.672
(1.00) 		0.899
(1.00) 		1
(1.00)
22q gain 9 (5%) 156 0.0417
(0.563) 		0.858
(1.00) 		0.575
(1.00) 		0.701
(1.00) 		0.391
(0.974) 		1
(1.00) 		1
(1.00) 		0.6
(1.00) 		1
(1.00) 		0.622
(1.00) 		0.357
(0.964) 		1
(1.00)
xp gain 34 (21%) 131 0.379
(0.974) 		0.452
(0.975) 		0.482
(0.978) 		0.376
(0.974) 		0.174
(0.828) 		0.265
(0.884) 		0.441
(0.974) 		0.353
(0.964) 		0.0718
(0.658) 		0.32
(0.915) 		0.57
(1.00) 		0.705
(1.00)
xq gain 34 (21%) 131 0.977
(1.00) 		0.284
(0.884) 		0.791
(1.00) 		0.209
(0.863) 		0.435
(0.974) 		0.586
(1.00) 		0.441
(0.974) 		0.356
(0.964) 		0.469
(0.978) 		0.926
(1.00) 		0.613
(1.00) 		0.692
(1.00)
1p loss 46 (28%) 119 0.295
(0.884) 		0.549
(0.996) 		0.881
(1.00) 		0.72
(1.00) 		0.555
(0.998) 		0.807
(1.00) 		0.489
(0.978) 		0.159
(0.812) 		0.0203
(0.531) 		0.884
(1.00) 		0.282
(0.884) 		0.102
(0.7)
1q loss 26 (16%) 139 0.941
(1.00) 		0.658
(1.00) 		0.67
(1.00) 		0.731
(1.00) 		0.572
(1.00) 		0.352
(0.964) 		0.284
(0.884) 		0.185
(0.843) 		0.224
(0.864) 		0.576
(1.00) 		0.504
(0.978) 		0.0074
(0.492)
2p loss 11 (7%) 154 0.674
(1.00) 		0.00649
(0.492) 		0.632
(1.00) 		0.607
(1.00) 		0.494
(0.978) 		1
(1.00) 		0.756
(1.00) 		0.648
(1.00) 		0.585
(1.00) 		0.72
(1.00) 		0.255
(0.884) 		1
(1.00)
2q loss 6 (4%) 159 0.319
(0.915) 		0.0267
(0.531) 		0.52
(0.987) 		1
(1.00) 		0.0682
(0.658) 		0.59
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.0279
(0.531)
3p loss 15 (9%) 150 0.00886
(0.492) 		0.673
(1.00) 		0.0479
(0.568) 		0.152
(0.805) 		0.206
(0.863) 		0.00725
(0.492) 		0.0544
(0.587) 		0.425
(0.974) 		0.0758
(0.67) 		0.013
(0.492) 		0.0537
(0.587) 		0.114
(0.718)
3q loss 10 (6%) 155 0.0158
(0.522) 		0.516
(0.987) 		0.0452
(0.563) 		0.392
(0.974) 		0.167
(0.819) 		0.0231
(0.531) 		0.11
(0.702) 		0.648
(1.00) 		0.00277
(0.492) 		0.0201
(0.531) 		0.0808
(0.674) 		0.116
(0.724)
4p loss 59 (36%) 106 0.0463
(0.563) 		0.6
(1.00) 		0.584
(1.00) 		0.517
(0.987) 		0.458
(0.975) 		0.821
(1.00) 		0.517
(0.987) 		0.0406
(0.563) 		0.381
(0.974) 		0.402
(0.974) 		0.286
(0.884) 		0.781
(1.00)
4q loss 66 (40%) 99 0.0221
(0.531) 		0.918
(1.00) 		0.49
(0.978) 		0.555
(0.998) 		0.734
(1.00) 		0.65
(1.00) 		0.339
(0.938) 		0.207
(0.863) 		0.253
(0.884) 		0.251
(0.884) 		0.535
(0.989) 		1
(1.00)
5p loss 26 (16%) 139 0.446
(0.975) 		0.93
(1.00) 		0.675
(1.00) 		0.847
(1.00) 		0.47
(0.978) 		1
(1.00) 		0.0916
(0.679) 		1
(1.00) 		0.696
(1.00) 		1
(1.00) 		0.241
(0.881) 		1
(1.00)
5q loss 40 (24%) 125 0.951
(1.00) 		0.145
(0.785) 		0.75
(1.00) 		0.669
(1.00) 		1
(1.00) 		0.609
(1.00) 		0.589
(1.00) 		0.777
(1.00) 		0.189
(0.843) 		0.57
(1.00) 		0.729
(1.00) 		0.707
(1.00)
6p loss 13 (8%) 152 0.105
(0.7) 		0.732
(1.00) 		0.124
(0.733) 		0.421
(0.974) 		0.0327
(0.531) 		0.694
(1.00) 		1
(1.00) 		0.394
(0.974) 		0.0613
(0.646) 		0.461
(0.975) 		0.236
(0.877) 		0.086
(0.679)
6q loss 22 (13%) 143 0.596
(1.00) 		0.838
(1.00) 		0.0279
(0.531) 		0.424
(0.974) 		0.0805
(0.674) 		1
(1.00) 		0.173
(0.828) 		0.327
(0.917) 		0.0127
(0.492) 		0.758
(1.00) 		0.803
(1.00) 		0.131
(0.733)
7q loss 3 (2%) 162 0.628
(1.00) 		0.227
(0.864) 		0.958
(1.00) 		0.683
(1.00) 		0.427
(0.974) 		1
(1.00) 		0.595
(1.00) 		0.312
(0.908) 		0.227
(0.864) 		1
(1.00) 		0.125
(0.733)
8p loss 73 (44%) 92 0.0702
(0.658) 		0.0897
(0.679) 		0.913
(1.00) 		0.579
(1.00) 		0.277
(0.884) 		0.825
(1.00) 		0.435
(0.974) 		0.615
(1.00) 		0.776
(1.00) 		0.956
(1.00) 		0.0718
(0.658) 		0.639
(1.00)
8q loss 11 (7%) 154 0.823
(1.00) 		0.468
(0.978) 		0.944
(1.00) 		0.371
(0.974) 		0.591
(1.00) 		0.689
(1.00) 		0.0117
(0.492) 		0.53
(0.988) 		0.602
(1.00) 		1
(1.00) 		0.943
(1.00) 		0.288
(0.884)
9p loss 23 (14%) 142 0.0407
(0.563) 		0.643
(1.00) 		0.166
(0.819) 		0.108
(0.7) 		1
(1.00) 		0.0596
(0.636) 		0.507
(0.978) 		0.717
(1.00) 		1
(1.00) 		0.00593
(0.492) 		0.505
(0.978) 		0.623
(1.00)
9q loss 23 (14%) 142 0.363
(0.972) 		0.6
(1.00) 		0.626
(1.00) 		0.0538
(0.587) 		0.694
(1.00) 		0.211
(0.863) 		0.507
(0.978) 		1
(1.00) 		1
(1.00) 		0.00897
(0.492) 		0.821
(1.00) 		0.623
(1.00)
10p loss 33 (20%) 132 0.0184
(0.531) 		0.0017
(0.492) 		0.522
(0.987) 		0.692
(1.00) 		0.868
(1.00) 		0.411
(0.974) 		0.699
(1.00) 		0.0244
(0.531) 		0.0252
(0.531) 		0.201
(0.863) 		0.354
(0.964) 		0.731
(1.00)
10q loss 38 (23%) 127 0.104
(0.7) 		0.0428
(0.563) 		0.504
(0.978) 		0.803
(1.00) 		0.969
(1.00) 		0.0673
(0.658) 		0.458
(0.975) 		0.0139
(0.492) 		0.0786
(0.673) 		0.16
(0.812) 		0.646
(1.00) 		0.743
(1.00)
11p loss 23 (14%) 142 0.459
(0.975) 		0.865
(1.00) 		0.0879
(0.679) 		0.449
(0.975) 		0.284
(0.884) 		0.53
(0.988) 		1
(1.00) 		0.733
(1.00) 		0.0728
(0.658) 		0.398
(0.974) 		0.0426
(0.563) 		0.165
(0.819)
11q loss 30 (18%) 135 0.576
(1.00) 		0.746
(1.00) 		0.688
(1.00) 		0.528
(0.988) 		0.963
(1.00) 		0.0804
(0.674) 		1
(1.00) 		0.235
(0.877) 		0.0404
(0.563) 		0.315
(0.914) 		0.713
(1.00) 		0.166
(0.819)
12p loss 22 (13%) 143 0.273
(0.884) 		0.555
(0.998) 		0.724
(1.00) 		0.652
(1.00) 		0.462
(0.975) 		0.53
(0.988) 		0.492
(0.978) 		0.733
(1.00) 		0.219
(0.863) 		1
(1.00) 		0.41
(0.974) 		1
(1.00)
12q loss 19 (12%) 146 0.295
(0.884) 		0.195
(0.861) 		0.654
(1.00) 		1
(1.00) 		0.55
(0.996) 		0.479
(0.978) 		0.809
(1.00) 		1
(1.00) 		0.365
(0.972) 		1
(1.00) 		0.394
(0.974) 		0.649
(1.00)
13q loss 8 (5%) 157 0.385
(0.974) 		0.805
(1.00) 		0.306
(0.895) 		0.6
(1.00) 		0.443
(0.974) 		0.615
(1.00) 		1
(1.00) 		0.269
(0.884) 		0.131
(0.733) 		0.623
(1.00) 		0.605
(1.00)
14q loss 67 (41%) 98 0.883
(1.00) 		0.858
(1.00) 		0.345
(0.951) 		0.55
(0.996) 		0.241
(0.881) 		0.823
(1.00) 		0.427
(0.974) 		0.0457
(0.563) 		0.0155
(0.522) 		0.215
(0.863) 		0.76
(1.00) 		0.395
(0.974)
15q loss 73 (44%) 92 0.721
(1.00) 		0.91
(1.00) 		0.303
(0.891) 		0.319
(0.915) 		0.442
(0.974) 		0.827
(1.00) 		0.16
(0.812) 		0.129
(0.733) 		1
(1.00) 		0.883
(1.00) 		0.0879
(0.679) 		1
(1.00)
16p loss 9 (5%) 156 0.778
(1.00) 		0.373
(0.974) 		0.0857
(0.679) 		0.843
(1.00) 		0.108
(0.7) 		1
(1.00) 		0.734
(1.00) 		1
(1.00) 		0.503
(0.978) 		1
(1.00) 		0.784
(1.00) 		1
(1.00)
16q loss 15 (9%) 150 0.574
(1.00) 		0.738
(1.00) 		0.25
(0.884) 		0.813
(1.00) 		0.0134
(0.492) 		0.47
(0.978) 		0.596
(1.00) 		0.394
(0.974) 		1
(1.00) 		0.757
(1.00) 		0.839
(1.00) 		1
(1.00)
17p loss 107 (65%) 58 0.582
(1.00) 		0.0761
(0.67) 		0.748
(1.00) 		0.036
(0.54) 		0.951
(1.00) 		1
(1.00) 		0.625
(1.00) 		0.296
(0.884) 		0.223
(0.864) 		0.654
(1.00) 		0.979
(1.00) 		0.611
(1.00)
17q loss 26 (16%) 139 0.273
(0.884) 		0.692
(1.00) 		0.739
(1.00) 		0.488
(0.978) 		0.747
(1.00) 		0.765
(1.00) 		0.831
(1.00) 		0.737
(1.00) 		1
(1.00) 		0.184
(0.841) 		0.393
(0.974) 		0.22
(0.863)
18p loss 128 (78%) 37 0.305
(0.895) 		0.413
(0.974) 		0.408
(0.974) 		0.259
(0.884) 		0.7
(1.00) 		0.108
(0.7) 		1
(1.00) 		1
(1.00) 		0.0294
(0.531) 		0.735
(1.00) 		0.548
(0.996) 		0.124
(0.733)
18q loss 138 (84%) 27 0.323
(0.915) 		0.263
(0.884) 		0.228
(0.864) 		0.0504
(0.569) 		0.757
(1.00) 		0.127
(0.733) 		0.674
(1.00) 		0.484
(0.978) 		0.432
(0.974) 		0.724
(1.00) 		0.646
(1.00) 		0.123
(0.733)
19p loss 21 (13%) 144 0.693
(1.00) 		0.769
(1.00) 		0.0292
(0.531) 		0.518
(0.987) 		0.283
(0.884) 		0.53
(0.988) 		1
(1.00) 		0.458
(0.975) 		0.368
(0.974) 		1
(1.00) 		0.0916
(0.679) 		1
(1.00)
19q loss 20 (12%) 145 0.734
(1.00) 		0.498
(0.978) 		0.0348
(0.539) 		0.256
(0.884) 		0.483
(0.978) 		0.739
(1.00) 		0.475
(0.978) 		1
(1.00) 		0.365
(0.972) 		0.613
(1.00) 		0.37
(0.974) 		1
(1.00)
20p loss 23 (14%) 142 0.761
(1.00) 		0.361
(0.971) 		0.0898
(0.679) 		0.598
(1.00) 		0.632
(1.00) 		1
(1.00) 		0.368
(0.974) 		0.46
(0.975) 		1
(1.00) 		0.242
(0.881) 		0.522
(0.987) 		0.175
(0.829)
21q loss 68 (41%) 97 0.744
(1.00) 		0.491
(0.978) 		0.713
(1.00) 		0.13
(0.733) 		0.278
(0.884) 		0.183
(0.841) 		0.636
(1.00) 		0.609
(1.00) 		0.242
(0.881) 		0.236
(0.877) 		0.186
(0.843) 		1
(1.00)
22q loss 58 (35%) 107 0.172
(0.827) 		0.102
(0.7) 		0.553
(0.998) 		0.415
(0.974) 		0.0103
(0.492) 		0.815
(1.00) 		0.871
(1.00) 		0.603
(1.00) 		1
(1.00) 		0.878
(1.00) 		0.125
(0.733) 		1
(1.00)
xp loss 25 (15%) 140 0.906
(1.00) 		0.973
(1.00) 		0.355
(0.964) 		0.217
(0.863) 		0.126
(0.733) 		0.765
(1.00) 		0.287
(0.884) 		0.327
(0.917) 		0.0974
(0.698) 		0.693
(1.00) 		0.23
(0.871) 		0.0727
(0.658)
xq loss 24 (15%) 141 0.888
(1.00) 		0.694
(1.00) 		0.443
(0.974) 		0.126
(0.733) 		0.41
(0.974) 		0.352
(0.964) 		0.268
(0.884) 		0.504
(0.978) 		0.404
(0.974) 		0.427
(0.974) 		0.451
(0.975) 		0.0871
(0.679)
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/READ-TP/19781849/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/READ-TP/19775480/READ-TP.merged_data.txt

  • Number of patients = 165

  • Number of significantly arm-level cnvs = 80

  • 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)
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