Correlation between copy number variations of arm-level result and selected clinical features
Rectum Adenocarcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
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 variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1V40TNN
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 11 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 11 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
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
1p gain 12 (7%) 153 0.144
(0.823)
0.564
(0.996)
0.157
(0.827)
0.0264
(0.582)
0.443
(0.996)
1
(1.00)
0.774
(1.00)
0.648
(0.996)
0.0483
(0.662)
0.217
(0.881)
0.588
(0.996)
1q gain 33 (20%) 132 0.463
(0.996)
0.61
(0.996)
0.297
(0.942)
0.00306
(0.444)
0.275
(0.919)
0.785
(1.00)
0.33
(0.98)
0.135
(0.814)
0.283
(0.933)
0.559
(0.996)
0.0587
(0.716)
2p gain 40 (24%) 125 0.497
(0.996)
0.674
(0.997)
0.518
(0.996)
0.386
(0.996)
0.159
(0.827)
0.432
(0.996)
0.0187
(0.542)
0.593
(0.996)
0.0395
(0.648)
0.0864
(0.73)
0.941
(1.00)
2q gain 41 (25%) 124 0.994
(1.00)
0.787
(1.00)
0.667
(0.997)
0.257
(0.9)
0.168
(0.833)
0.445
(0.996)
0.0311
(0.588)
0.42
(0.996)
0.0222
(0.542)
0.148
(0.827)
0.97
(1.00)
3p gain 27 (16%) 138 0.257
(0.9)
0.819
(1.00)
0.192
(0.879)
0.848
(1.00)
0.411
(0.996)
0.226
(0.887)
0.533
(0.996)
0.525
(0.996)
0.698
(1.00)
0.885
(1.00)
0.198
(0.881)
3q gain 33 (20%) 132 0.444
(0.996)
0.903
(1.00)
0.373
(0.996)
0.856
(1.00)
0.427
(0.996)
0.399
(0.996)
0.33
(0.98)
0.558
(0.996)
0.305
(0.949)
0.717
(1.00)
0.296
(0.942)
4p gain 9 (5%) 156 0.558
(0.996)
0.914
(1.00)
0.746
(1.00)
0.554
(0.996)
0.245
(0.898)
1
(1.00)
0.18
(0.852)
1
(1.00)
1
(1.00)
1
(1.00)
0.0286
(0.588)
4q gain 5 (3%) 160 0.962
(1.00)
0.857
(1.00)
0.803
(1.00)
1
(1.00)
0.707
(1.00)
0.59
(0.996)
0.0626
(0.716)
1
(1.00)
1
(1.00)
1
(1.00)
0.447
(0.996)
5p gain 35 (21%) 130 0.748
(1.00)
0.772
(1.00)
0.547
(0.996)
0.234
(0.892)
0.582
(0.996)
0.588
(0.996)
0.13
(0.813)
0.25
(0.898)
0.0734
(0.716)
0.359
(0.996)
0.401
(0.996)
5q gain 24 (15%) 141 0.653
(0.996)
0.936
(1.00)
0.168
(0.833)
0.602
(0.996)
0.298
(0.942)
0.757
(1.00)
0.386
(0.996)
0.315
(0.966)
0.22
(0.881)
0.541
(0.996)
0.2
(0.881)
6p gain 40 (24%) 125 0.0655
(0.716)
0.571
(0.996)
0.158
(0.827)
0.256
(0.9)
0.0314
(0.588)
0.0611
(0.716)
0.467
(0.996)
0.396
(0.996)
0.189
(0.873)
0.826
(1.00)
0.045
(0.648)
6q gain 35 (21%) 130 0.346
(0.995)
0.873
(1.00)
0.00831
(0.444)
0.445
(0.996)
0.0202
(0.542)
0.00857
(0.444)
0.45
(0.996)
0.545
(0.996)
0.0721
(0.716)
0.216
(0.881)
0.0417
(0.648)
7p gain 102 (62%) 63 0.502
(0.996)
0.628
(0.996)
0.107
(0.791)
0.41
(0.996)
0.133
(0.813)
0.649
(0.996)
0.63
(0.996)
1
(1.00)
0.00466
(0.444)
0.385
(0.996)
0.0374
(0.643)
7q gain 87 (53%) 78 0.564
(0.996)
0.47
(0.996)
0.005
(0.444)
0.528
(0.996)
0.0489
(0.662)
0.268
(0.903)
0.535
(0.996)
0.468
(0.996)
0.0068
(0.444)
0.199
(0.881)
0.0792
(0.716)
8p gain 40 (24%) 125 0.953
(1.00)
0.98
(1.00)
0.0638
(0.716)
0.245
(0.898)
0.382
(0.996)
0.291
(0.942)
0.716
(1.00)
0.771
(1.00)
1
(1.00)
0.112
(0.805)
0.338
(0.989)
8q gain 90 (55%) 75 0.0428
(0.648)
0.529
(0.996)
0.00629
(0.444)
0.151
(0.827)
0.103
(0.791)
0.0728
(0.716)
0.877
(1.00)
0.813
(1.00)
0.0855
(0.73)
0.0193
(0.542)
0.163
(0.827)
9p gain 43 (26%) 122 0.105
(0.791)
0.218
(0.881)
0.483
(0.996)
0.851
(1.00)
0.718
(1.00)
0.617
(0.996)
1
(1.00)
0.589
(0.996)
0.331
(0.98)
0.426
(0.996)
0.991
(1.00)
9q gain 35 (21%) 130 0.351
(0.996)
0.131
(0.813)
0.105
(0.791)
0.967
(1.00)
0.902
(1.00)
0.786
(1.00)
0.706
(1.00)
0.565
(0.996)
0.478
(0.996)
0.808
(1.00)
0.659
(0.997)
10p gain 12 (7%) 153 0.893
(1.00)
0.91
(1.00)
0.925
(1.00)
0.578
(0.996)
0.726
(1.00)
0.691
(1.00)
0.774
(1.00)
0.607
(0.996)
0.601
(0.996)
1
(1.00)
0.4
(0.996)
10q gain 7 (4%) 158 0.724
(1.00)
0.51
(0.996)
0.709
(1.00)
0.682
(1.00)
0.876
(1.00)
1
(1.00)
0.25
(0.898)
1
(1.00)
1
(1.00)
1
(1.00)
0.993
(1.00)
11p gain 32 (19%) 133 0.147
(0.827)
0.469
(0.996)
0.998
(1.00)
0.57
(0.996)
0.72
(1.00)
0.785
(1.00)
0.845
(1.00)
0.763
(1.00)
0.0724
(0.716)
1
(1.00)
0.296
(0.942)
11q gain 27 (16%) 138 0.093
(0.765)
0.123
(0.813)
0.921
(1.00)
0.401
(0.996)
0.559
(0.996)
0.242
(0.898)
1
(1.00)
0.737
(1.00)
0.127
(0.813)
0.794
(1.00)
0.234
(0.892)
12p gain 33 (20%) 132 0.895
(1.00)
0.421
(0.996)
0.781
(1.00)
0.376
(0.996)
0.361
(0.996)
0.415
(0.996)
0.699
(1.00)
0.0727
(0.716)
0.298
(0.942)
0.397
(0.996)
0.524
(0.996)
12q gain 21 (13%) 144 0.454
(0.996)
0.281
(0.929)
0.958
(1.00)
0.206
(0.881)
0.429
(0.996)
1
(1.00)
0.641
(0.996)
0.467
(0.996)
1
(1.00)
0.853
(1.00)
0.246
(0.898)
13q gain 114 (69%) 51 0.729
(1.00)
0.715
(1.00)
0.259
(0.9)
0.158
(0.827)
0.0143
(0.526)
0.814
(1.00)
0.404
(0.996)
0.3
(0.942)
0.000486
(0.292)
0.955
(1.00)
0.0106
(0.519)
14q gain 8 (5%) 157 0.457
(0.996)
0.894
(1.00)
0.721
(1.00)
1
(1.00)
0.399
(0.996)
1
(1.00)
0.472
(0.996)
0.566
(0.996)
1
(1.00)
1
(1.00)
0.628
(0.996)
15q gain 4 (2%) 161 0.114
(0.808)
0.518
(0.996)
0.343
(0.995)
0.0987
(0.782)
0.177
(0.844)
1
(1.00)
0.335
(0.985)
0.392
(0.996)
0.0339
(0.621)
1
(1.00)
0.526
(0.996)
16p gain 41 (25%) 124 0.259
(0.9)
0.777
(1.00)
0.121
(0.813)
0.734
(1.00)
0.272
(0.914)
0.798
(1.00)
1
(1.00)
0.411
(0.996)
0.0222
(0.542)
0.393
(0.996)
0.276
(0.919)
16q gain 41 (25%) 124 0.97
(1.00)
0.853
(1.00)
0.409
(0.996)
0.958
(1.00)
0.128
(0.813)
0.291
(0.942)
0.857
(1.00)
1
(1.00)
0.0222
(0.542)
0.623
(0.996)
0.2
(0.881)
17p gain 10 (6%) 155 0.22
(0.881)
0.927
(1.00)
0.537
(0.996)
0.0161
(0.526)
0.418
(0.996)
0.638
(0.996)
0.754
(1.00)
1
(1.00)
0.585
(0.996)
0.714
(1.00)
1
(1.00)
17q gain 31 (19%) 134 0.514
(0.996)
0.777
(1.00)
0.915
(1.00)
0.799
(1.00)
0.177
(0.844)
0.162
(0.827)
0.691
(1.00)
0.764
(1.00)
0.466
(0.996)
0.518
(0.996)
0.65
(0.996)
18p gain 8 (5%) 157 0.127
(0.813)
0.425
(0.996)
0.151
(0.827)
0.373
(0.996)
0.496
(0.996)
1
(1.00)
0.727
(1.00)
0.0446
(0.648)
0.131
(0.813)
0.152
(0.827)
0.238
(0.893)
18q gain 6 (4%) 159 0.0546
(0.696)
0.391
(0.996)
0.127
(0.813)
0.162
(0.827)
0.0854
(0.73)
0.509
(0.996)
0.219
(0.881)
0.0247
(0.558)
0.406
(0.996)
0.0477
(0.662)
0.0288
(0.588)
19p gain 33 (20%) 132 0.634
(0.996)
0.732
(1.00)
0.816
(1.00)
0.344
(0.995)
0.812
(1.00)
0.588
(0.996)
0.559
(0.996)
0.76
(1.00)
0.0718
(0.716)
0.497
(0.996)
0.854
(1.00)
19q gain 33 (20%) 132 0.226
(0.887)
0.672
(0.997)
0.833
(1.00)
0.336
(0.985)
0.87
(1.00)
0.279
(0.928)
0.559
(0.996)
0.525
(0.996)
0.0718
(0.716)
0.262
(0.9)
0.802
(1.00)
20p gain 105 (64%) 60 0.762
(1.00)
0.525
(0.996)
0.0146
(0.526)
0.5
(0.996)
0.416
(0.996)
0.249
(0.898)
0.33
(0.98)
0.607
(0.996)
0.0672
(0.716)
0.511
(0.996)
0.46
(0.996)
20q gain 146 (88%) 19 0.479
(0.996)
0.235
(0.892)
0.207
(0.881)
0.602
(0.996)
0.038
(0.643)
0.308
(0.956)
1
(1.00)
0.723
(1.00)
0.000663
(0.292)
0.184
(0.859)
0.162
(0.827)
21q gain 10 (6%) 155 0.788
(1.00)
0.482
(0.996)
0.561
(0.996)
0.741
(1.00)
0.904
(1.00)
0.638
(0.996)
1
(1.00)
1
(1.00)
1
(1.00)
0.674
(0.997)
0.913
(1.00)
22q gain 9 (5%) 156 0.197
(0.881)
0.858
(1.00)
0.583
(0.996)
0.699
(1.00)
0.391
(0.996)
1
(1.00)
1
(1.00)
0.594
(0.996)
1
(1.00)
0.624
(0.996)
0.346
(0.995)
xp gain 31 (19%) 134 0.48
(0.996)
0.566
(0.996)
0.353
(0.996)
0.299
(0.942)
0.083
(0.73)
0.138
(0.82)
0.32
(0.975)
0.362
(0.996)
0.13
(0.813)
0.264
(0.9)
0.459
(0.996)
xq gain 32 (19%) 133 0.965
(1.00)
0.553
(0.996)
0.868
(1.00)
0.125
(0.813)
0.35
(0.996)
0.399
(0.996)
0.432
(0.996)
0.365
(0.996)
0.465
(0.996)
0.855
(1.00)
0.5
(0.996)
1p loss 46 (28%) 119 0.481
(0.996)
0.549
(0.996)
0.838
(1.00)
0.712
(1.00)
0.587
(0.996)
0.808
(1.00)
0.489
(0.996)
0.433
(0.996)
0.0203
(0.542)
0.883
(1.00)
0.341
(0.993)
1q loss 28 (17%) 137 0.526
(0.996)
0.476
(0.996)
0.669
(0.997)
0.598
(0.996)
0.816
(1.00)
0.545
(0.996)
0.145
(0.823)
0.752
(1.00)
0.127
(0.813)
0.618
(0.996)
0.922
(1.00)
2p loss 11 (7%) 154 0.534
(0.996)
0.00649
(0.444)
0.642
(0.996)
0.648
(0.996)
0.494
(0.996)
1
(1.00)
0.756
(1.00)
0.648
(0.996)
0.585
(0.996)
0.718
(1.00)
0.263
(0.9)
2q loss 7 (4%) 158 0.248
(0.898)
0.0611
(0.716)
0.551
(0.996)
1
(1.00)
0.134
(0.813)
0.598
(0.996)
0.704
(1.00)
1
(1.00)
1
(1.00)
1
(1.00)
0.176
(0.844)
3p loss 15 (9%) 150 0.0507
(0.676)
0.673
(0.997)
0.106
(0.791)
0.189
(0.873)
0.142
(0.823)
0.00454
(0.444)
0.0544
(0.696)
0.416
(0.996)
0.0758
(0.716)
0.0124
(0.526)
0.0515
(0.677)
3q loss 10 (6%) 155 0.0689
(0.716)
0.516
(0.996)
0.141
(0.823)
0.418
(0.996)
0.168
(0.833)
0.0236
(0.55)
0.11
(0.797)
0.625
(0.996)
0.00277
(0.444)
0.0205
(0.542)
0.0786
(0.716)
4p loss 60 (36%) 105 0.134
(0.813)
0.799
(1.00)
0.573
(0.996)
0.769
(1.00)
0.322
(0.976)
0.82
(1.00)
0.629
(0.996)
0.209
(0.881)
0.77
(1.00)
0.396
(0.996)
0.155
(0.827)
4q loss 67 (41%) 98 0.0871
(0.73)
0.715
(1.00)
0.437
(0.996)
0.713
(1.00)
0.573
(0.996)
0.649
(0.996)
0.427
(0.996)
0.624
(0.996)
0.567
(0.996)
0.217
(0.881)
0.408
(0.996)
5p loss 27 (16%) 138 0.665
(0.997)
0.982
(1.00)
0.982
(1.00)
0.866
(1.00)
0.591
(0.996)
1
(1.00)
0.145
(0.823)
1
(1.00)
0.698
(1.00)
1
(1.00)
0.432
(0.996)
5q loss 40 (24%) 125 0.649
(0.996)
0.145
(0.823)
0.603
(0.996)
0.685
(1.00)
1
(1.00)
0.61
(0.996)
0.589
(0.996)
0.401
(0.996)
0.189
(0.873)
0.568
(0.996)
0.759
(1.00)
6p loss 14 (8%) 151 0.0372
(0.643)
0.928
(1.00)
0.0921
(0.764)
0.381
(0.996)
0.0238
(0.55)
1
(1.00)
0.786
(1.00)
0.111
(0.797)
0.0758
(0.716)
0.33
(0.98)
0.456
(0.996)
6q loss 23 (14%) 142 0.987
(1.00)
0.605
(0.996)
0.12
(0.813)
0.325
(0.98)
0.068
(0.716)
1
(1.00)
0.268
(0.903)
0.103
(0.791)
0.0159
(0.526)
0.777
(1.00)
0.672
(0.997)
7q loss 3 (2%) 162 0.538
(0.996)
0.227
(0.887)
0.951
(1.00)
0.675
(0.997)
0.43
(0.996)
1
(1.00)
0.595
(0.996)
0.392
(0.996)
0.227
(0.887)
1
(1.00)
0.126
(0.813)
8p loss 75 (45%) 90 0.064
(0.716)
0.152
(0.827)
0.719
(1.00)
0.841
(1.00)
0.163
(0.827)
1
(1.00)
0.642
(0.996)
1
(1.00)
0.773
(1.00)
0.956
(1.00)
0.0446
(0.648)
8q loss 10 (6%) 155 0.883
(1.00)
0.808
(1.00)
0.755
(1.00)
0.201
(0.881)
0.828
(1.00)
1
(1.00)
0.00194
(0.444)
1
(1.00)
1
(1.00)
1
(1.00)
0.718
(1.00)
9p loss 23 (14%) 142 0.251
(0.898)
0.643
(0.996)
0.117
(0.813)
0.0969
(0.775)
1
(1.00)
0.0608
(0.716)
0.507
(0.996)
0.723
(1.00)
1
(1.00)
0.00564
(0.444)
0.489
(0.996)
9q loss 23 (14%) 142 0.472
(0.996)
0.6
(0.996)
0.511
(0.996)
0.0469
(0.662)
0.697
(1.00)
0.213
(0.881)
0.507
(0.996)
1
(1.00)
1
(1.00)
0.00811
(0.444)
0.842
(1.00)
10p loss 34 (21%) 131 0.0155
(0.526)
0.00343
(0.444)
0.426
(0.996)
0.705
(1.00)
0.736
(1.00)
0.291
(0.942)
0.567
(0.996)
0.0369
(0.643)
0.0294
(0.588)
0.181
(0.854)
0.255
(0.9)
10q loss 38 (23%) 127 0.0699
(0.716)
0.0428
(0.648)
0.447
(0.996)
0.802
(1.00)
1
(1.00)
0.0668
(0.716)
0.458
(0.996)
0.0212
(0.542)
0.0786
(0.716)
0.159
(0.827)
0.618
(0.996)
11p loss 24 (15%) 141 0.938
(1.00)
0.609
(0.996)
0.118
(0.813)
0.198
(0.881)
0.173
(0.842)
0.529
(0.996)
1
(1.00)
0.167
(0.833)
0.0846
(0.73)
0.401
(0.996)
0.0161
(0.526)
11q loss 30 (18%) 135 0.717
(1.00)
0.746
(1.00)
0.725
(1.00)
0.511
(0.996)
0.963
(1.00)
0.0797
(0.716)
1
(1.00)
0.227
(0.887)
0.0404
(0.648)
0.319
(0.974)
0.688
(1.00)
12p loss 23 (14%) 142 0.086
(0.73)
0.513
(0.996)
0.489
(0.996)
0.576
(0.996)
0.634
(0.996)
0.749
(1.00)
0.653
(0.996)
0.737
(1.00)
0.217
(0.881)
1
(1.00)
0.522
(0.996)
12q loss 24 (15%) 141 0.209
(0.881)
0.142
(0.823)
0.265
(0.9)
0.849
(1.00)
1
(1.00)
0.757
(1.00)
0.665
(0.997)
0.505
(0.996)
0.694
(1.00)
1
(1.00)
0.673
(0.997)
13q loss 6 (4%) 159 0.301
(0.942)
0.764
(1.00)
0.335
(0.985)
0.738
(1.00)
0.736
(1.00)
1
(1.00)
0.416
(0.996)
0.109
(0.797)
0.077
(0.716)
0.5
(0.996)
0.726
(1.00)
14q loss 67 (41%) 98 0.41
(0.996)
0.858
(1.00)
0.548
(0.996)
0.663
(0.997)
0.228
(0.887)
0.824
(1.00)
0.427
(0.996)
0.215
(0.881)
0.0155
(0.526)
0.21
(0.881)
0.716
(1.00)
15q loss 72 (44%) 93 0.742
(1.00)
0.954
(1.00)
0.42
(0.996)
0.424
(0.996)
0.408
(0.996)
1
(1.00)
0.21
(0.881)
0.633
(0.996)
0.778
(1.00)
0.882
(1.00)
0.0777
(0.716)
16p loss 9 (5%) 156 0.865
(1.00)
0.373
(0.996)
0.291
(0.942)
0.37
(0.996)
0.0945
(0.768)
1
(1.00)
0.734
(1.00)
1
(1.00)
0.503
(0.996)
1
(1.00)
0.795
(1.00)
16q loss 14 (8%) 151 0.646
(0.996)
0.531
(0.996)
0.625
(0.996)
0.909
(1.00)
0.0144
(0.526)
0.694
(1.00)
0.786
(1.00)
0.416
(0.996)
1
(1.00)
0.752
(1.00)
0.962
(1.00)
17p loss 105 (64%) 60 0.653
(0.996)
0.125
(0.813)
0.658
(0.997)
0.0415
(0.648)
0.843
(1.00)
1
(1.00)
0.42
(0.996)
0.62
(0.996)
0.23
(0.888)
0.811
(1.00)
0.925
(1.00)
17q loss 28 (17%) 137 0.866
(1.00)
0.945
(1.00)
0.45
(0.996)
0.63
(0.996)
0.576
(0.996)
0.767
(1.00)
0.299
(0.942)
0.76
(1.00)
1
(1.00)
0.172
(0.842)
0.515
(0.996)
18p loss 128 (78%) 37 0.206
(0.881)
0.413
(0.996)
0.63
(0.996)
0.356
(0.996)
0.635
(0.996)
0.107
(0.791)
1
(1.00)
0.771
(1.00)
0.0294
(0.588)
0.737
(1.00)
0.467
(0.996)
18q loss 138 (84%) 27 0.372
(0.996)
0.263
(0.9)
0.668
(0.997)
0.0951
(0.768)
0.757
(1.00)
0.127
(0.813)
0.674
(0.997)
0.315
(0.966)
0.432
(0.996)
0.723
(1.00)
0.54
(0.996)
19p loss 24 (15%) 141 0.674
(0.997)
0.846
(1.00)
0.171
(0.842)
0.779
(1.00)
0.492
(0.996)
0.536
(0.996)
0.825
(1.00)
0.304
(0.949)
0.217
(0.881)
1
(1.00)
0.176
(0.844)
19q loss 22 (13%) 143 0.863
(1.00)
0.444
(0.996)
0.265
(0.9)
0.73
(1.00)
0.463
(0.996)
0.529
(0.996)
0.492
(0.996)
0.737
(1.00)
0.374
(0.996)
0.509
(0.996)
0.645
(0.996)
20p loss 24 (15%) 141 0.328
(0.98)
0.5
(0.996)
0.0311
(0.588)
0.578
(0.996)
0.588
(0.996)
0.531
(0.996)
1
(1.00)
0.243
(0.898)
1
(1.00)
0.508
(0.996)
0.796
(1.00)
21q loss 68 (41%) 97 0.97
(1.00)
0.491
(0.996)
0.638
(0.996)
0.159
(0.827)
0.232
(0.89)
0.258
(0.9)
0.636
(0.996)
0.62
(0.996)
0.242
(0.898)
0.237
(0.893)
0.216
(0.881)
22q loss 58 (35%) 107 0.25
(0.898)
0.102
(0.791)
0.539
(0.996)
0.469
(0.996)
0.00777
(0.444)
0.645
(0.996)
0.871
(1.00)
0.802
(1.00)
1
(1.00)
0.877
(1.00)
0.151
(0.827)
xp loss 28 (17%) 137 0.66
(0.997)
0.806
(1.00)
0.648
(0.996)
0.294
(0.942)
0.136
(0.814)
1
(1.00)
0.411
(0.996)
0.315
(0.966)
0.23
(0.888)
0.791
(1.00)
0.208
(0.881)
xq loss 26 (16%) 139 0.793
(1.00)
0.872
(1.00)
0.661
(0.997)
0.0596
(0.716)
0.561
(0.996)
0.545
(0.996)
0.207
(0.881)
0.489
(0.996)
0.432
(0.996)
0.539
(0.996)
0.408
(0.996)
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/22532765/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/READ-TP/22507018/READ-TP.merged_data.txt

  • Number of patients = 165

  • Number of significantly arm-level cnvs = 80

  • Number of selected clinical features = 11

  • 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)