Correlation between copy number variations of arm-level result and selected clinical features
Mesothelioma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C1930SF7
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/C1930SF7
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 74 arm-level events and 11 clinical features across 87 patients, 3 significant findings detected with Q value < 0.25.

  • 7q gain cnv correlated to 'PATHOLOGY_N_STAGE'.

  • 9q gain cnv correlated to 'Time to Death'.

  • 10q loss 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 74 arm-level events and 11 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 3 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 		KARNOFSKY
PERFORMANCE
SCORE 		HISTOLOGICAL
TYPE 		RESIDUAL
TUMOR
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 Fisher's exact test Fisher's exact test
7q gain 22 (25%) 65 0.397
(1.00) 		0.336
(1.00) 		0.458
(1.00) 		0.732
(1.00) 		0.00044
(0.179) 		0.545
(1.00) 		0.538
(1.00) 		0.59
(1.00) 		1
(1.00) 		0.951
(1.00) 		0.206
(1.00)
9q gain 4 (5%) 83 0.000818
(0.222) 		0.223
(1.00) 		0.51
(1.00) 		0.249
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.698
(1.00)
10q loss 19 (22%) 68 0.000214
(0.174) 		0.662
(1.00) 		0.168
(1.00) 		0.486
(1.00) 		0.654
(1.00) 		0.099
(1.00) 		0.505
(1.00) 		0.778
(1.00) 		0.192
(1.00) 		0.496
(1.00) 		0.347
(1.00)
1p gain 10 (11%) 77 0.108
(1.00) 		0.372
(1.00) 		0.466
(1.00) 		0.813
(1.00) 		0.458
(1.00) 		1
(1.00) 		1
(1.00) 		0.164
(1.00) 		0.222
(1.00) 		0.175
(1.00)
1q gain 21 (24%) 66 0.221
(1.00) 		0.909
(1.00) 		0.63
(1.00) 		0.607
(1.00) 		0.881
(1.00) 		0.544
(1.00) 		0.522
(1.00) 		0.402
(1.00) 		0.00767
(0.831) 		0.469
(1.00) 		0.71
(1.00)
2p gain 4 (5%) 83 0.736
(1.00) 		0.655
(1.00) 		0.216
(1.00) 		0.471
(1.00) 		1
(1.00) 		1
(1.00) 		0.563
(1.00) 		1
(1.00) 		0.078
(1.00)
2q gain 7 (8%) 80 0.806
(1.00) 		0.851
(1.00) 		0.33
(1.00) 		0.818
(1.00) 		0.867
(1.00) 		1
(1.00) 		1
(1.00) 		0.431
(1.00) 		0.223
(1.00) 		0.563
(1.00)
3p gain 17 (20%) 70 0.402
(1.00) 		0.524
(1.00) 		0.0536
(1.00) 		0.332
(1.00) 		0.741
(1.00) 		1
(1.00) 		0.506
(1.00) 		0.768
(1.00) 		1
(1.00) 		0.504
(1.00) 		0.481
(1.00)
3q gain 19 (22%) 68 0.206
(1.00) 		0.611
(1.00) 		0.0432
(1.00) 		0.311
(1.00) 		0.705
(1.00) 		0.558
(1.00) 		0.327
(1.00) 		1
(1.00) 		0.407
(1.00) 		0.428
(1.00) 		0.257
(1.00)
5p gain 24 (28%) 63 0.946
(1.00) 		0.374
(1.00) 		0.801
(1.00) 		0.148
(1.00) 		0.344
(1.00) 		1
(1.00) 		0.761
(1.00) 		0.59
(1.00) 		0.798
(1.00) 		0.727
(1.00) 		0.344
(1.00)
5q gain 15 (17%) 72 0.783
(1.00) 		0.779
(1.00) 		0.643
(1.00) 		0.0674
(1.00) 		0.536
(1.00) 		1
(1.00) 		0.463
(1.00) 		0.752
(1.00) 		0.869
(1.00) 		0.393
(1.00) 		0.789
(1.00)
6p gain 7 (8%) 80 0.0619
(1.00) 		0.612
(1.00) 		0.402
(1.00) 		0.171
(1.00) 		0.133
(1.00) 		1
(1.00) 		0.608
(1.00) 		0.192
(1.00) 		0.644
(1.00) 		0.819
(1.00) 		0.651
(1.00)
6q gain 4 (5%) 83 0.545
(1.00) 		0.243
(1.00) 		0.106
(1.00) 		0.0474
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.0822
(1.00) 		1
(1.00) 		0.861
(1.00)
7p gain 25 (29%) 62 0.413
(1.00) 		0.398
(1.00) 		0.385
(1.00) 		0.933
(1.00) 		0.00137
(0.259) 		0.545
(1.00) 		0.769
(1.00) 		0.794
(1.00) 		1
(1.00) 		0.634
(1.00) 		0.332
(1.00)
8p gain 12 (14%) 75 0.376
(1.00) 		0.534
(1.00) 		0.667
(1.00) 		0.101
(1.00) 		0.585
(1.00) 		1
(1.00) 		0.452
(1.00) 		1
(1.00) 		0.825
(1.00) 		0.503
(1.00) 		0.927
(1.00)
8q gain 14 (16%) 73 0.869
(1.00) 		0.544
(1.00) 		0.203
(1.00) 		0.078
(1.00) 		0.495
(1.00) 		0.462
(1.00) 		0.451
(1.00) 		0.522
(1.00) 		0.494
(1.00) 		0.667
(1.00) 		0.745
(1.00)
9p gain 3 (3%) 84 0.919
(1.00) 		0.0675
(1.00) 		0.462
(1.00) 		0.0743
(1.00) 		0.702
(1.00) 		1
(1.00) 		1
(1.00) 		0.219
(1.00) 		1
(1.00)
10p gain 3 (3%) 84 0.943
(1.00) 		0.322
(1.00) 		0.125
(1.00) 		0.291
(1.00) 		0.363
(1.00) 		1
(1.00) 		0.461
(1.00) 		1
(1.00) 		0.105
(1.00) 		0.815
(1.00)
10q gain 3 (3%) 84 0.943
(1.00) 		0.322
(1.00) 		0.122
(1.00) 		0.294
(1.00) 		0.362
(1.00) 		1
(1.00) 		0.461
(1.00) 		1
(1.00) 		0.104
(1.00) 		0.816
(1.00)
11p gain 11 (13%) 76 0.974
(1.00) 		0.454
(1.00) 		0.863
(1.00) 		0.785
(1.00) 		0.0666
(1.00) 		1
(1.00) 		0.681
(1.00) 		0.164
(1.00) 		0.0881
(1.00) 		0.928
(1.00)
11q gain 12 (14%) 75 0.294
(1.00) 		0.183
(1.00) 		0.913
(1.00) 		0.829
(1.00) 		0.0957
(1.00) 		1
(1.00) 		0.452
(1.00) 		0.297
(1.00) 		0.895
(1.00) 		0.0601
(1.00) 		0.927
(1.00)
12p gain 18 (21%) 69 0.274
(1.00) 		0.809
(1.00) 		0.322
(1.00) 		0.697
(1.00) 		0.154
(1.00) 		1
(1.00) 		0.506
(1.00) 		0.778
(1.00) 		0.435
(1.00) 		0.924
(1.00)
12q gain 18 (21%) 69 0.274
(1.00) 		0.809
(1.00) 		0.32
(1.00) 		0.698
(1.00) 		0.156
(1.00) 		1
(1.00) 		0.506
(1.00) 		0.778
(1.00) 		0.433
(1.00) 		0.923
(1.00)
13q gain 5 (6%) 82 0.475
(1.00) 		0.763
(1.00) 		0.442
(1.00) 		0.63
(1.00) 		0.416
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
15q gain 11 (13%) 76 0.58
(1.00) 		0.934
(1.00) 		0.241
(1.00) 		0.228
(1.00) 		0.81
(1.00) 		1
(1.00) 		0.417
(1.00) 		1
(1.00) 		0.692
(1.00) 		1
(1.00) 		0.749
(1.00)
16p gain 17 (20%) 70 0.876
(1.00) 		0.202
(1.00) 		0.3
(1.00) 		1
(1.00) 		0.0893
(1.00) 		1
(1.00) 		0.728
(1.00) 		0.372
(1.00) 		0.295
(1.00) 		0.203
(1.00) 		0.265
(1.00)
16q gain 16 (18%) 71 0.857
(1.00) 		0.194
(1.00) 		0.268
(1.00) 		0.818
(1.00) 		0.309
(1.00) 		1
(1.00) 		1
(1.00) 		0.372
(1.00) 		0.295
(1.00) 		0.293
(1.00) 		0.0264
(0.831)
17p gain 7 (8%) 80 0.923
(1.00) 		0.0619
(1.00) 		0.31
(1.00) 		0.679
(1.00) 		0.867
(1.00) 		1
(1.00) 		0.34
(1.00) 		1
(1.00) 		0.138
(1.00) 		1
(1.00)
17q gain 17 (20%) 70 0.968
(1.00) 		0.5
(1.00) 		0.542
(1.00) 		0.96
(1.00) 		0.166
(1.00) 		0.566
(1.00) 		0.728
(1.00) 		0.551
(1.00) 		0.0701
(1.00) 		0.737
(1.00)
18p gain 8 (9%) 79 0.478
(1.00) 		0.78
(1.00) 		0.446
(1.00) 		1
(1.00) 		0.663
(1.00) 		1
(1.00) 		0.636
(1.00) 		1
(1.00) 		0.332
(1.00) 		0.862
(1.00)
18q gain 4 (5%) 83 0.3
(1.00) 		0.887
(1.00) 		0.153
(1.00) 		0.75
(1.00) 		1
(1.00) 		1
(1.00) 		0.563
(1.00) 		0.582
(1.00) 		0.145
(1.00) 		0.862
(1.00)
19p gain 14 (16%) 73 0.742
(1.00) 		0.37
(1.00) 		0.697
(1.00) 		0.889
(1.00) 		0.396
(1.00) 		1
(1.00) 		1
(1.00) 		0.172
(1.00) 		0.114
(1.00) 		0.509
(1.00) 		0.747
(1.00)
19q gain 10 (11%) 77 0.568
(1.00) 		0.263
(1.00) 		0.252
(1.00) 		0.64
(1.00) 		0.692
(1.00) 		1
(1.00) 		0.681
(1.00) 		0.239
(1.00) 		0.391
(1.00) 		0.321
(1.00) 		1
(1.00)
20p gain 8 (9%) 79 0.263
(1.00) 		0.494
(1.00) 		0.187
(1.00) 		0.868
(1.00) 		0.631
(1.00) 		1
(1.00) 		1
(1.00) 		0.695
(1.00) 		0.452
(1.00) 		0.649
(1.00)
20q gain 10 (11%) 77 0.874
(1.00) 		0.665
(1.00) 		0.211
(1.00) 		0.965
(1.00) 		0.693
(1.00) 		1
(1.00) 		0.197
(1.00) 		0.484
(1.00) 		1
(1.00) 		0.928
(1.00)
21q gain 6 (7%) 81 0.167
(1.00) 		0.154
(1.00) 		0.925
(1.00) 		0.828
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.363
(1.00) 		0.025
(0.831) 		1
(1.00) 		0.11
(1.00)
xp gain 7 (8%) 80 0.92
(1.00) 		0.382
(1.00) 		0.946
(1.00) 		0.815
(1.00) 		0.45
(1.00) 		1
(1.00) 		0.608
(1.00) 		0.67
(1.00) 		1
(1.00) 		0.0328
(0.86)
xq gain 6 (7%) 81 0.754
(1.00) 		0.476
(1.00) 		0.688
(1.00) 		0.598
(1.00) 		0.305
(1.00) 		1
(1.00) 		0.304
(1.00) 		1
(1.00) 		0.801
(1.00) 		0.0853
(1.00)
1p loss 8 (9%) 79 0.169
(1.00) 		0.982
(1.00) 		0.47
(1.00) 		0.315
(1.00) 		0.366
(1.00) 		1
(1.00) 		0.16
(1.00) 		1
(1.00) 		0.844
(1.00) 		0.159
(1.00)
2p loss 6 (7%) 81 0.252
(1.00) 		0.383
(1.00) 		1
(1.00) 		0.828
(1.00) 		0.713
(1.00) 		1
(1.00) 		0.304
(1.00) 		0.17
(1.00) 		0.166
(1.00) 		0.141
(1.00)
2q loss 4 (5%) 83 0.408
(1.00) 		0.753
(1.00) 		1
(1.00) 		0.911
(1.00) 		1
(1.00) 		1
(1.00) 		0.0187
(0.831) 		0.308
(1.00) 		0.697
(1.00) 		0.0518
(1.00)
3p loss 8 (9%) 79 0.363
(1.00) 		0.895
(1.00) 		0.259
(1.00) 		0.865
(1.00) 		0.316
(1.00) 		1
(1.00) 		0.342
(1.00) 		0.239
(1.00) 		0.843
(1.00) 		0.652
(1.00)
3q loss 6 (7%) 81 0.478
(1.00) 		0.0826
(1.00) 		0.0993
(1.00) 		0.601
(1.00) 		0.293
(1.00) 		1
(1.00) 		0.587
(1.00) 		0.363
(1.00) 		0.168
(1.00) 		1
(1.00)
4p loss 32 (37%) 55 0.102
(1.00) 		0.271
(1.00) 		0.871
(1.00) 		0.648
(1.00) 		0.402
(1.00) 		0.258
(1.00) 		0.573
(1.00) 		0.462
(1.00) 		0.213
(1.00) 		0.189
(1.00) 		0.0231
(0.831)
4q loss 33 (38%) 54 0.102
(1.00) 		0.291
(1.00) 		0.705
(1.00) 		0.135
(1.00) 		0.269
(1.00) 		0.268
(1.00) 		0.393
(1.00) 		0.804
(1.00) 		0.0471
(1.00) 		0.22
(1.00) 		0.00982
(0.831)
5p loss 4 (5%) 83 0.0465
(1.00) 		0.648
(1.00) 		0.885
(1.00) 		0.536
(1.00) 		1
(1.00) 		1
(1.00) 		0.563
(1.00) 		0.0822
(1.00) 		0.697
(1.00) 		0.816
(1.00)
5q loss 9 (10%) 78 0.0652
(1.00) 		0.712
(1.00) 		0.81
(1.00) 		1
(1.00) 		0.409
(1.00) 		1
(1.00) 		1
(1.00) 		0.123
(1.00) 		0.871
(1.00) 		0.885
(1.00)
6p loss 9 (10%) 78 0.0531
(1.00) 		0.0645
(1.00) 		0.00292
(0.396) 		0.328
(1.00) 		0.525
(1.00) 		1
(1.00) 		0.201
(1.00) 		0.424
(1.00) 		0.309
(1.00) 		0.886
(1.00)
6q loss 29 (33%) 58 0.264
(1.00) 		0.953
(1.00) 		0.00835
(0.831) 		0.428
(1.00) 		0.139
(1.00) 		1
(1.00) 		1
(1.00) 		0.798
(1.00) 		0.0873
(1.00) 		0.641
(1.00) 		0.378
(1.00)
8p loss 13 (15%) 74 0.235
(1.00) 		0.283
(1.00) 		0.205
(1.00) 		0.608
(1.00) 		1
(1.00) 		0.427
(1.00) 		1
(1.00) 		0.201
(1.00) 		0.262
(1.00) 		0.15
(1.00) 		0.025
(0.831)
8q loss 4 (5%) 83 0.48
(1.00) 		0.655
(1.00) 		0.0207
(0.831) 		0.0896
(1.00) 		1
(1.00) 		1
(1.00) 		0.563
(1.00) 		0.582
(1.00) 		0.0813
(1.00) 		0.13
(1.00)
9p loss 28 (32%) 59 0.00159
(0.259) 		0.669
(1.00) 		0.413
(1.00) 		0.22
(1.00) 		0.793
(1.00) 		0.551
(1.00) 		0.249
(1.00) 		1
(1.00) 		0.813
(1.00) 		0.334
(1.00) 		0.652
(1.00)
9q loss 21 (24%) 66 0.031
(0.841) 		0.893
(1.00) 		0.313
(1.00) 		0.936
(1.00) 		0.182
(1.00) 		1
(1.00) 		0.337
(1.00) 		0.573
(1.00) 		0.62
(1.00) 		0.473
(1.00) 		1
(1.00)
10p loss 24 (28%) 63 0.0157
(0.831) 		0.628
(1.00) 		0.487
(1.00) 		0.831
(1.00) 		0.767
(1.00) 		0.556
(1.00) 		0.0593
(1.00) 		0.791
(1.00) 		0.058
(1.00) 		0.533
(1.00) 		0.697
(1.00)
11p loss 4 (5%) 83 0.201
(1.00) 		0.147
(1.00) 		0.0166
(0.831) 		0.386
(1.00) 		0.702
(1.00) 		1
(1.00) 		0.563
(1.00) 		1
(1.00) 		0.0527
(1.00) 		0.815
(1.00)
11q loss 5 (6%) 82 0.0261
(0.831) 		0.391
(1.00) 		0.0192
(0.831) 		0.149
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.308
(1.00) 		0.0219
(0.831) 		0.816
(1.00)
12p loss 4 (5%) 83 0.136
(1.00) 		0.081
(1.00) 		0.508
(1.00) 		1
(1.00) 		0.246
(1.00) 		1
(1.00) 		0.563
(1.00) 		0.582
(1.00) 		0.188
(1.00)
13q loss 33 (38%) 54 0.0104
(0.831) 		0.612
(1.00) 		0.477
(1.00) 		0.955
(1.00) 		0.592
(1.00) 		0.0591
(1.00) 		0.776
(1.00) 		0.804
(1.00) 		0.724
(1.00) 		0.967
(1.00) 		0.835
(1.00)
14q loss 35 (40%) 52 0.0307
(0.841) 		0.24
(1.00) 		0.164
(1.00) 		0.03
(0.841) 		0.168
(1.00) 		0.258
(1.00) 		0.0532
(1.00) 		0.808
(1.00) 		0.113
(1.00) 		0.0194
(0.831) 		0.748
(1.00)
15q loss 11 (13%) 76 0.0132
(0.831) 		0.462
(1.00) 		0.134
(1.00) 		0.572
(1.00) 		0.458
(1.00) 		1
(1.00) 		0.681
(1.00) 		0.297
(1.00) 		0.111
(1.00) 		1
(1.00)
16p loss 7 (8%) 80 0.577
(1.00) 		0.167
(1.00) 		0.0764
(1.00) 		0.209
(1.00) 		0.03
(0.841) 		1
(1.00) 		1
(1.00) 		0.662
(1.00) 		0.157
(1.00) 		0.408
(1.00)
16q loss 10 (11%) 77 0.349
(1.00) 		0.241
(1.00) 		0.0129
(0.831) 		0.155
(1.00) 		0.0382
(0.972) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.223
(1.00) 		0.0635
(1.00)
17p loss 23 (26%) 64 0.307
(1.00) 		0.0182
(0.831) 		0.448
(1.00) 		0.204
(1.00) 		0.0766
(1.00) 		0.556
(1.00) 		0.754
(1.00) 		1
(1.00) 		0.687
(1.00) 		0.911
(1.00) 		1
(1.00)
17q loss 7 (8%) 80 0.791
(1.00) 		0.725
(1.00) 		0.135
(1.00) 		0.164
(1.00) 		1
(1.00) 		1
(1.00) 		0.608
(1.00) 		0.662
(1.00) 		0.391
(1.00) 		0.679
(1.00) 		0.213
(1.00)
18p loss 9 (10%) 78 0.44
(1.00) 		0.244
(1.00) 		0.76
(1.00) 		1
(1.00) 		0.782
(1.00) 		1
(1.00) 		1
(1.00) 		0.0946
(1.00) 		0.578
(1.00) 		0.177
(1.00)
18q loss 14 (16%) 73 0.291
(1.00) 		0.945
(1.00) 		0.609
(1.00) 		0.594
(1.00) 		0.914
(1.00) 		1
(1.00) 		0.124
(1.00) 		0.328
(1.00) 		0.926
(1.00) 		0.365
(1.00)
19p loss 4 (5%) 83 0.457
(1.00) 		0.367
(1.00) 		0.131
(1.00) 		1
(1.00) 		0.226
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.699
(1.00)
19q loss 7 (8%) 80 0.217
(1.00) 		0.857
(1.00) 		0.135
(1.00) 		0.713
(1.00) 		0.582
(1.00) 		1
(1.00) 		1
(1.00) 		0.67
(1.00) 		1
(1.00) 		0.271
(1.00)
20p loss 14 (16%) 73 0.43
(1.00) 		0.949
(1.00) 		0.297
(1.00) 		0.73
(1.00) 		0.383
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.692
(1.00) 		0.137
(1.00) 		0.0265
(0.831)
20q loss 3 (3%) 84 0.181
(1.00) 		0.196
(1.00) 		0.195
(1.00) 		0.54
(1.00) 		1
(1.00) 		1
(1.00) 		0.461
(1.00) 		0.549
(1.00) 		0.104
(1.00)
21q loss 11 (13%) 76 0.117
(1.00) 		0.954
(1.00) 		0.078
(1.00) 		0.332
(1.00) 		0.694
(1.00) 		1
(1.00) 		0.681
(1.00) 		0.269
(1.00) 		0.366
(1.00) 		0.455
(1.00)
22q loss 67 (77%) 20 0.172
(1.00) 		0.936
(1.00) 		0.462
(1.00) 		0.229
(1.00) 		0.867
(1.00) 		0.556
(1.00) 		0.511
(1.00) 		0.279
(1.00) 		0.377
(1.00) 		0.452
(1.00) 		0.852
(1.00)
xp loss 27 (31%) 60 0.577
(1.00) 		0.24
(1.00) 		0.967
(1.00) 		0.879
(1.00) 		0.89
(1.00) 		0.212
(1.00) 		0.766
(1.00) 		0.603
(1.00) 		0.838
(1.00) 		0.416
(1.00) 		0.719
(1.00)
xq loss 28 (32%) 59 0.501
(1.00) 		0.298
(1.00) 		0.939
(1.00) 		0.837
(1.00) 		0.896
(1.00) 		0.233
(1.00) 		0.568
(1.00) 		0.311
(1.00) 		0.838
(1.00) 		0.405
(1.00) 		1
(1.00)
'7q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00044 (Fisher's exact test), Q value = 0.18

Table S1.  Gene #12: '7q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2+N3
ALL 44 10 29
7Q GAIN MUTATED 7 0 15
7Q GAIN WILD-TYPE 37 10 14

Figure S1.  Get High-res Image Gene #12: '7q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'9q gain' versus 'Time to Death'

P value = 0.000818 (logrank test), Q value = 0.22

Table S2.  Gene #16: '9q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 86 71 0.7 - 91.7 (16.9)
9Q GAIN MUTATED 4 4 2.8 - 11.8 (6.5)
9Q GAIN WILD-TYPE 82 67 0.7 - 91.7 (17.8)

Figure S2.  Get High-res Image Gene #16: '9q gain' versus Clinical Feature #1: 'Time to Death'

'10q loss' versus 'Time to Death'

P value = 0.000214 (logrank test), Q value = 0.17

Table S3.  Gene #54: '10q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 86 71 0.7 - 91.7 (16.9)
10Q LOSS MUTATED 19 16 0.7 - 20.0 (10.8)
10Q LOSS WILD-TYPE 67 55 1.3 - 91.7 (21.4)

Figure S3.  Get High-res Image Gene #54: '10q loss' versus Clinical Feature #1: 'Time to Death'

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/MESO-TP/19781626/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/MESO-TP/19775385/MESO-TP.merged_data.txt

  • Number of patients = 87

  • Number of significantly arm-level cnvs = 74

  • 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)
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