Correlation between copy number variations of arm-level result and selected clinical features
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 results and 11 clinical features across 131 patients, 9 significant findings detected with Q value < 0.25.

  • 2p gain cnv correlated to 'GENDER'.

  • 4p gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

  • 5q gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

  • 9q gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

  • 14q gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

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

  • 17p gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

  • 6p loss cnv correlated to 'KARNOFSKY.PERFORMANCE.SCORE'.

  • 16q loss cnv correlated to 'TOBACCOSMOKINGHISTORYINDICATOR'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 74 arm-level results and 11 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 9 significant findings detected.

Clinical
Features 		Time
to
Death 		AGE GENDER KARNOFSKY
PERFORMANCE
SCORE 		NUMBERPACKYEARSSMOKED TOBACCOSMOKINGHISTORYINDICATOR DISTANT
METASTASIS 		LYMPH
NODE
METASTASIS 		NUMBER
OF
LYMPH
NODES 		TUMOR
STAGECODE 		NEOPLASM
DISEASESTAGE
nCNV (%) nWild-Type logrank test t-test Fisher's exact test t-test t-test t-test Fisher's exact test Chi-square test t-test t-test Fisher's exact test
2p gain 0 (0%) 106 0.584
(1.00) 		0.595
(1.00) 		0.000227
(0.156) 		0.934
(1.00) 		0.741
(1.00) 		0.356
(1.00) 		1
(1.00) 		0.437
(1.00) 		0.492
(1.00) 		0.684
(1.00)
4p gain 0 (0%) 123 0.0892
(1.00) 		0.819
(1.00) 		0.679
(1.00) 		0.394
(1.00) 		0.000201
(0.138)
5q gain 0 (0%) 114 0.16
(1.00) 		0.55
(1.00) 		0.237
(1.00) 		0.252
(1.00) 		0.914
(1.00) 		0.913
(1.00) 		0.823
(1.00) 		0.377
(1.00) 		0.000102
(0.0701) 		0.367
(1.00)
9q gain 0 (0%) 119 0.0825
(1.00) 		0.186
(1.00) 		0.496
(1.00) 		0.786
(1.00) 		0.167
(1.00) 		0.975
(1.00) 		0.691
(1.00) 		0.402
(1.00) 		2.87e-06
(0.00199) 		0.00942
(1.00)
14q gain 0 (0%) 120 0.955
(1.00) 		0.633
(1.00) 		0.467
(1.00) 		0.471
(1.00) 		0.341
(1.00) 		0.728
(1.00) 		0.736
(1.00) 		0.747
(1.00) 		7.1e-05
(0.0489) 		0.689
(1.00)
16p gain 0 (0%) 122 4.1e-05
(0.0284) 		0.484
(1.00) 		0.228
(1.00) 		0.45
(1.00) 		0.212
(1.00) 		0.721
(1.00) 		0.263
(1.00) 		0.853
(1.00) 		0.068
(1.00) 		0.61
(1.00)
17p gain 0 (0%) 124 0.305
(1.00) 		0.972
(1.00) 		0.367
(1.00) 		0.974
(1.00) 		0.535
(1.00) 		0.691
(1.00) 		0.402
(1.00) 		3.04e-06
(0.00211) 		0.12
(1.00)
6p loss 0 (0%) 113 0.994
(1.00) 		0.348
(1.00) 		0.775
(1.00) 		6.63e-05
(0.0457) 		0.655
(1.00) 		0.341
(1.00) 		0.345
(1.00) 		0.264
(1.00) 		0.282
(1.00) 		0.0307
(1.00)
16q loss 0 (0%) 116 0.718
(1.00) 		0.31
(1.00) 		0.354
(1.00) 		0.191
(1.00) 		0.946
(1.00) 		4.43e-05
(0.0306) 		0.813
(1.00) 		0.0107
(1.00) 		0.344
(1.00) 		0.215
(1.00)
1p gain 0 (0%) 116 0.083
(1.00) 		0.501
(1.00) 		0.528
(1.00) 		0.494
(1.00) 		0.429
(1.00) 		0.976
(1.00) 		0.783
(1.00) 		0.463
(1.00) 		0.558
(1.00) 		0.226
(1.00)
1q gain 0 (0%) 102 0.029
(1.00) 		0.0223
(1.00) 		0.809
(1.00) 		0.257
(1.00) 		0.675
(1.00) 		0.845
(1.00) 		0.572
(1.00) 		0.911
(1.00) 		0.849
(1.00) 		0.699
(1.00)
2q gain 0 (0%) 121 0.62
(1.00) 		0.632
(1.00) 		0.712
(1.00) 		0.257
(1.00) 		0.443
(1.00) 		0.716
(1.00) 		0.551
(1.00) 		0.434
(1.00) 		0.316
(1.00) 		0.0363
(1.00)
3p gain 0 (0%) 105 0.485
(1.00) 		0.507
(1.00) 		0.459
(1.00) 		0.422
(1.00) 		0.87
(1.00) 		0.938
(1.00) 		0.742
(1.00) 		0.374
(1.00) 		0.262
(1.00) 		0.265
(1.00)
3q gain 0 (0%) 94 0.207
(1.00) 		0.25
(1.00) 		0.119
(1.00) 		0.846
(1.00) 		0.872
(1.00) 		0.707
(1.00) 		0.643
(1.00) 		0.503
(1.00) 		0.27
(1.00) 		0.61
(1.00)
4q gain 0 (0%) 128 0.303
(1.00) 		0.515
(1.00) 		1
(1.00) 		0.284
(1.00)
5p gain 0 (0%) 92 0.797
(1.00) 		0.488
(1.00) 		0.512
(1.00) 		0.135
(1.00) 		0.581
(1.00) 		0.567
(1.00) 		0.602
(1.00) 		0.0104
(1.00) 		0.31
(1.00) 		0.507
(1.00)
6p gain 0 (0%) 121 0.205
(1.00) 		0.643
(1.00) 		1
(1.00) 		0.616
(1.00) 		0.669
(1.00) 		0.886
(1.00) 		1
(1.00) 		0.447
(1.00) 		0.122
(1.00) 		0.893
(1.00)
6q gain 0 (0%) 126 0.105
(1.00) 		0.895
(1.00) 		0.33
(1.00) 		0.779
(1.00) 		0.00639
(1.00)
7p gain 0 (0%) 93 0.497
(1.00) 		0.344
(1.00) 		0.516
(1.00) 		0.141
(1.00) 		0.413
(1.00) 		0.0177
(1.00) 		0.361
(1.00) 		0.954
(1.00) 		0.788
(1.00) 		1
(1.00)
7q gain 0 (0%) 96 0.583
(1.00) 		0.631
(1.00) 		0.0238
(1.00) 		0.141
(1.00) 		0.256
(1.00) 		0.127
(1.00) 		0.88
(1.00) 		0.879
(1.00) 		0.535
(1.00) 		0.508
(1.00)
8p gain 0 (0%) 117 0.902
(1.00) 		0.185
(1.00) 		1
(1.00) 		0.821
(1.00) 		0.214
(1.00) 		0.304
(1.00) 		1
(1.00) 		0.834
(1.00) 		0.0016
(1.00) 		0.867
(1.00)
8q gain 0 (0%) 92 0.558
(1.00) 		0.573
(1.00) 		0.827
(1.00) 		0.896
(1.00) 		0.322
(1.00) 		0.715
(1.00) 		0.635
(1.00) 		0.993
(1.00) 		0.165
(1.00) 		0.74
(1.00)
9p gain 0 (0%) 118 0.037
(1.00) 		0.0242
(1.00) 		0.183
(1.00) 		0.842
(1.00) 		0.0265
(1.00) 		0.119
(1.00) 		0.744
(1.00) 		0.319
(1.00) 		0.00161
(1.00) 		0.489
(1.00)
10p gain 0 (0%) 106 0.87
(1.00) 		0.993
(1.00) 		0.614
(1.00) 		0.73
(1.00) 		0.56
(1.00) 		0.372
(1.00) 		1
(1.00) 		0.607
(1.00) 		0.666
(1.00) 		0.801
(1.00)
10q gain 0 (0%) 124 0.402
(1.00) 		0.113
(1.00) 		1
(1.00) 		0.689
(1.00) 		0.648
(1.00) 		0.609
(1.00) 		0.866
(1.00) 		0.535
(1.00)
11p gain 0 (0%) 125 0.0551
(1.00) 		0.109
(1.00) 		0.336
(1.00) 		0.0875
(1.00) 		0.618
(1.00) 		0.183
(1.00) 		1
(1.00) 		0.217
(1.00) 		0.1
(1.00) 		0.523
(1.00)
11q gain 0 (0%) 124 0.297
(1.00) 		0.301
(1.00) 		0.191
(1.00) 		0.792
(1.00) 		0.997
(1.00) 		0.649
(1.00) 		1
(1.00) 		0.302
(1.00) 		0.321
(1.00) 		0.737
(1.00)
12p gain 0 (0%) 107 0.847
(1.00) 		0.723
(1.00) 		1
(1.00) 		0.245
(1.00) 		0.978
(1.00) 		0.699
(1.00) 		0.713
(1.00) 		0.446
(1.00) 		0.0101
(1.00) 		0.374
(1.00)
12q gain 0 (0%) 114 0.36
(1.00) 		0.464
(1.00) 		0.237
(1.00) 		0.347
(1.00) 		0.532
(1.00) 		0.561
(1.00) 		0.422
(1.00) 		0.553
(1.00) 		0.0816
(1.00) 		0.427
(1.00)
13q gain 0 (0%) 110 0.383
(1.00) 		0.597
(1.00) 		1
(1.00) 		0.64
(1.00) 		0.145
(1.00) 		0.672
(1.00) 		0.165
(1.00) 		0.174
(1.00) 		0.871
(1.00) 		0.481
(1.00)
15q gain 0 (0%) 127 0.0836
(1.00) 		0.828
(1.00) 		1
(1.00) 		0.922
(1.00)
16q gain 0 (0%) 119 0.00157
(1.00) 		0.319
(1.00) 		0.0733
(1.00) 		0.468
(1.00) 		0.439
(1.00) 		0.0896
(1.00) 		0.483
(1.00) 		0.849
(1.00) 		0.0525
(1.00) 		0.489
(1.00)
17q gain 0 (0%) 109 0.691
(1.00) 		0.923
(1.00) 		0.792
(1.00) 		0.0945
(1.00) 		0.438
(1.00) 		0.0874
(1.00) 		1
(1.00) 		0.882
(1.00) 		0.936
(1.00) 		1
(1.00)
18p gain 0 (0%) 110 0.885
(1.00) 		0.99
(1.00) 		0.785
(1.00) 		0.469
(1.00) 		0.375
(1.00) 		0.0858
(1.00) 		0.705
(1.00) 		0.623
(1.00) 		0.679
(1.00) 		1
(1.00)
18q gain 0 (0%) 124 0.026
(1.00) 		0.788
(1.00) 		1
(1.00) 		0.848
(1.00) 		0.232
(1.00) 		0.664
(1.00) 		0.838
(1.00) 		0.269
(1.00) 		1
(1.00)
19p gain 0 (0%) 120 0.631
(1.00) 		0.892
(1.00) 		0.729
(1.00) 		0.257
(1.00) 		0.377
(1.00) 		0.834
(1.00) 		0.776
(1.00) 		0.648
(1.00) 		0.0478
(1.00) 		0.279
(1.00)
19q gain 0 (0%) 107 0.327
(1.00) 		0.962
(1.00) 		0.309
(1.00) 		0.345
(1.00) 		0.4
(1.00) 		0.83
(1.00) 		1
(1.00) 		0.919
(1.00) 		0.731
(1.00) 		0.431
(1.00)
20p gain 0 (0%) 83 0.324
(1.00) 		0.844
(1.00) 		0.143
(1.00) 		0.753
(1.00) 		0.435
(1.00) 		0.992
(1.00) 		0.609
(1.00) 		0.367
(1.00) 		0.419
(1.00) 		0.876
(1.00)
20q gain 0 (0%) 78 0.734
(1.00) 		0.387
(1.00) 		1
(1.00) 		0.48
(1.00) 		0.279
(1.00) 		0.558
(1.00) 		0.559
(1.00) 		0.503
(1.00) 		0.402
(1.00) 		0.508
(1.00)
21q gain 0 (0%) 107 0.437
(1.00) 		0.216
(1.00) 		1
(1.00) 		0.907
(1.00) 		0.639
(1.00) 		0.492
(1.00) 		0.813
(1.00) 		0.677
(1.00) 		0.929
(1.00) 		0.259
(1.00)
22q gain 0 (0%) 120 0.0761
(1.00) 		0.544
(1.00) 		0.729
(1.00) 		0.606
(1.00) 		0.487
(1.00) 		0.0612
(1.00) 		0.551
(1.00) 		0.405
(1.00) 		0.54
(1.00) 		0.689
(1.00)
Xq gain 0 (0%) 125 0.43
(1.00) 		0.7
(1.00) 		0.641
(1.00) 		0.473
(1.00) 		0.472
(1.00) 		0.455
(1.00) 		0.167
(1.00) 		0.0933
(1.00) 		0.523
(1.00)
2p loss 0 (0%) 124 0.588
(1.00) 		0.654
(1.00) 		0.679
(1.00) 		0.904
(1.00) 		0.238
(1.00) 		0.983
(1.00) 		0.691
(1.00) 		0.167
(1.00) 		0.523
(1.00)
2q loss 0 (0%) 116 0.0327
(1.00) 		0.985
(1.00) 		0.354
(1.00) 		0.904
(1.00) 		0.226
(1.00) 		0.677
(1.00) 		0.813
(1.00) 		0.0296
(1.00) 		0.13
(1.00) 		0.0898
(1.00)
3p loss 0 (0%) 122 0.943
(1.00) 		0.645
(1.00) 		0.228
(1.00) 		0.494
(1.00) 		0.957
(1.00) 		1
(1.00) 		0.597
(1.00) 		0.862
(1.00) 		0.361
(1.00)
4p loss 0 (0%) 106 0.503
(1.00) 		0.922
(1.00) 		1
(1.00) 		0.0948
(1.00) 		0.541
(1.00) 		0.434
(1.00) 		0.497
(1.00) 		0.0965
(1.00) 		0.261
(1.00) 		0.371
(1.00)
4q loss 0 (0%) 107 0.682
(1.00) 		0.738
(1.00) 		0.795
(1.00) 		0.0948
(1.00) 		0.905
(1.00) 		0.305
(1.00) 		0.462
(1.00) 		0.944
(1.00) 		0.807
(1.00) 		0.941
(1.00)
5p loss 0 (0%) 120 0.225
(1.00) 		0.452
(1.00) 		0.143
(1.00) 		0.0998
(1.00) 		0.802
(1.00) 		0.41
(1.00) 		0.736
(1.00) 		0.946
(1.00) 		0.973
(1.00) 		0.293
(1.00)
5q loss 0 (0%) 101 0.854
(1.00) 		0.61
(1.00) 		0.632
(1.00) 		0.305
(1.00) 		0.345
(1.00) 		0.391
(1.00) 		0.346
(1.00) 		0.182
(1.00) 		0.291
(1.00) 		0.129
(1.00)
6q loss 0 (0%) 104 0.332
(1.00) 		0.906
(1.00) 		0.62
(1.00) 		0.148
(1.00) 		0.374
(1.00) 		0.377
(1.00) 		0.316
(1.00) 		0.216
(1.00) 		0.286
(1.00) 		0.132
(1.00)
8p loss 0 (0%) 85 0.352
(1.00) 		0.464
(1.00) 		0.301
(1.00) 		0.41
(1.00) 		0.149
(1.00) 		0.835
(1.00) 		0.91
(1.00) 		0.57
(1.00) 		0.863
(1.00) 		0.843
(1.00)
8q loss 0 (0%) 125 0.957
(1.00) 		0.0819
(1.00) 		0.641
(1.00) 		0.847
(1.00) 		0.98
(1.00) 		0.691
(1.00) 		0.582
(1.00) 		0.894
(1.00) 		0.215
(1.00)
9p loss 0 (0%) 93 0.982
(1.00) 		0.58
(1.00) 		0.278
(1.00) 		0.374
(1.00) 		0.284
(1.00) 		0.526
(1.00) 		0.22
(1.00) 		0.478
(1.00) 		0.892
(1.00) 		0.422
(1.00)
9q loss 0 (0%) 95 0.812
(1.00) 		0.876
(1.00) 		0.185
(1.00) 		0.651
(1.00) 		0.198
(1.00) 		0.886
(1.00) 		0.291
(1.00) 		0.609
(1.00) 		0.0671
(1.00) 		0.409
(1.00)
10p loss 0 (0%) 113 0.481
(1.00) 		0.896
(1.00) 		1
(1.00) 		0.0186
(1.00) 		0.804
(1.00) 		0.224
(1.00) 		0.559
(1.00) 		0.388
(1.00) 		0.0409
(1.00) 		0.932
(1.00)
10q loss 0 (0%) 105 0.427
(1.00) 		0.0231
(1.00) 		0.805
(1.00) 		0.134
(1.00) 		0.744
(1.00) 		0.766
(1.00) 		0.778
(1.00) 		0.671
(1.00) 		0.849
(1.00) 		0.772
(1.00)
11p loss 0 (0%) 89 0.617
(1.00) 		0.271
(1.00) 		0.833
(1.00) 		0.135
(1.00) 		0.982
(1.00) 		0.249
(1.00) 		0.243
(1.00) 		0.789
(1.00) 		0.241
(1.00) 		0.336
(1.00)
11q loss 0 (0%) 100 0.882
(1.00) 		0.619
(1.00) 		0.815
(1.00) 		0.708
(1.00) 		0.343
(1.00) 		0.884
(1.00) 		0.536
(1.00) 		0.794
(1.00) 		0.258
(1.00) 		0.724
(1.00)
12p loss 0 (0%) 126 0.937
(1.00) 		0.298
(1.00) 		0.33
(1.00) 		0.678
(1.00) 		0.39
(1.00) 		1
(1.00) 		0.619
(1.00) 		0.877
(1.00) 		0.387
(1.00)
12q loss 0 (0%) 125 0.125
(1.00) 		0.314
(1.00) 		0.336
(1.00) 		0.857
(1.00) 		0.318
(1.00) 		1
(1.00) 		0.0362
(1.00) 		0.462
(1.00) 		0.195
(1.00)
13q loss 0 (0%) 113 0.874
(1.00) 		0.685
(1.00) 		0.24
(1.00) 		0.0159
(1.00) 		0.723
(1.00) 		0.308
(1.00) 		1
(1.00) 		0.481
(1.00) 		0.582
(1.00) 		0.387
(1.00)
14q loss 0 (0%) 109 0.21
(1.00) 		0.241
(1.00) 		0.28
(1.00) 		0.772
(1.00) 		0.719
(1.00) 		0.677
(1.00) 		1
(1.00) 		0.406
(1.00) 		0.676
(1.00) 		0.849
(1.00)
15q loss 0 (0%) 116 0.472
(1.00) 		0.824
(1.00) 		0.528
(1.00) 		0.763
(1.00) 		0.883
(1.00) 		0.00922
(1.00) 		1
(1.00) 		0.755
(1.00) 		0.946
(1.00) 		0.518
(1.00)
16p loss 0 (0%) 117 0.459
(1.00) 		0.205
(1.00) 		0.188
(1.00) 		0.0945
(1.00) 		0.443
(1.00) 		0.00096
(0.655) 		1
(1.00) 		0.137
(1.00) 		0.976
(1.00) 		0.649
(1.00)
17p loss 0 (0%) 94 0.392
(1.00) 		0.602
(1.00) 		0.824
(1.00) 		0.856
(1.00) 		0.338
(1.00) 		0.73
(1.00) 		0.716
(1.00) 		0.711
(1.00) 		0.769
(1.00) 		0.777
(1.00)
17q loss 0 (0%) 126 0.887
(1.00) 		0.407
(1.00) 		1
(1.00) 		0.77
(1.00) 		0.526
(1.00) 		0.29
(1.00) 		1
(1.00) 		0.0247
(1.00) 		0.0658
(1.00)
18p loss 0 (0%) 113 0.329
(1.00) 		0.0554
(1.00) 		0.392
(1.00) 		0.295
(1.00) 		0.674
(1.00) 		0.892
(1.00) 		0.189
(1.00) 		0.867
(1.00) 		0.847
(1.00) 		0.684
(1.00)
18q loss 0 (0%) 97 0.0978
(1.00) 		0.0375
(1.00) 		0.167
(1.00) 		0.57
(1.00) 		0.253
(1.00) 		0.565
(1.00) 		0.635
(1.00) 		0.929
(1.00) 		0.824
(1.00) 		0.777
(1.00)
19p loss 0 (0%) 123 0.341
(1.00) 		0.913
(1.00) 		1
(1.00) 		0.929
(1.00) 		0.641
(1.00) 		0.0861
(1.00) 		0.00234
(1.00) 		0.265
(1.00) 		0.00166
(1.00)
19q loss 0 (0%) 128 0.000889
(0.608) 		0.9
(1.00) 		0.572
(1.00) 		0.692
(1.00)
20p loss 0 (0%) 126 0.714
(1.00) 		0.479
(1.00) 		1
(1.00) 		0.0292
(1.00) 		0.9
(1.00) 		0.64
(1.00) 		0.538
(1.00)
21q loss 0 (0%) 118 0.996
(1.00) 		0.000838
(0.574) 		1
(1.00) 		0.00136
(0.928) 		0.894
(1.00) 		0.397
(1.00) 		0.295
(1.00) 		0.00863
(1.00) 		0.616
(1.00) 		0.0642
(1.00)
22q loss 0 (0%) 106 0.115
(1.00) 		0.518
(1.00) 		0.799
(1.00) 		0.187
(1.00) 		0.808
(1.00) 		0.264
(1.00) 		0.859
(1.00) 		0.711
(1.00) 		0.627
(1.00) 		0.888
(1.00)
Xq loss 0 (0%) 128 0.31
(1.00) 		0.858
(1.00) 		1
(1.00) 		0.349
(1.00) 		0.0942
(1.00) 		1
(1.00) 		0.0658
(1.00)
'2p gain' versus 'GENDER'

P value = 0.000227 (Fisher's exact test), Q value = 0.16

Table S1.  Gene #3: '2p gain' versus Clinical Feature #3: 'GENDER'

nPatients FEMALE MALE
ALL 33 98
2P GAIN CNV 14 11
2P GAIN WILD-TYPE 19 87

Figure S1.  Get High-res Image Gene #3: '2p gain' versus Clinical Feature #3: 'GENDER'

'4p gain' versus 'NUMBER.OF.LYMPH.NODES'

P value = 0.000201 (t-test), Q value = 0.14

Table S2.  Gene #7: '4p gain' versus Clinical Feature #9: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 98 1.9 (3.8)
4P GAIN CNV 5 0.2 (0.4)
4P GAIN WILD-TYPE 93 2.0 (3.8)

Figure S2.  Get High-res Image Gene #7: '4p gain' versus Clinical Feature #9: 'NUMBER.OF.LYMPH.NODES'

'5q gain' versus 'NUMBER.OF.LYMPH.NODES'

P value = 0.000102 (t-test), Q value = 0.07

Table S3.  Gene #10: '5q gain' versus Clinical Feature #9: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 98 1.9 (3.8)
5Q GAIN CNV 11 0.3 (0.5)
5Q GAIN WILD-TYPE 87 2.1 (3.9)

Figure S3.  Get High-res Image Gene #10: '5q gain' versus Clinical Feature #9: 'NUMBER.OF.LYMPH.NODES'

'9q gain' versus 'NUMBER.OF.LYMPH.NODES'

P value = 2.87e-06 (t-test), Q value = 0.002

Table S4.  Gene #18: '9q gain' versus Clinical Feature #9: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 98 1.9 (3.8)
9Q GAIN CNV 9 0.0 (0.0)
9Q GAIN WILD-TYPE 89 2.1 (3.9)

Figure S4.  Get High-res Image Gene #18: '9q gain' versus Clinical Feature #9: 'NUMBER.OF.LYMPH.NODES'

'14q gain' versus 'NUMBER.OF.LYMPH.NODES'

P value = 7.1e-05 (t-test), Q value = 0.049

Table S5.  Gene #26: '14q gain' versus Clinical Feature #9: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 98 1.9 (3.8)
14Q GAIN CNV 6 0.2 (0.4)
14Q GAIN WILD-TYPE 92 2.0 (3.9)

Figure S5.  Get High-res Image Gene #26: '14q gain' versus Clinical Feature #9: 'NUMBER.OF.LYMPH.NODES'

'16p gain' versus 'Time to Death'

P value = 4.1e-05 (logrank test), Q value = 0.028

Table S6.  Gene #28: '16p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 124 32 0.1 - 131.2 (7.0)
16P GAIN CNV 9 5 2.2 - 9.7 (5.1)
16P GAIN WILD-TYPE 115 27 0.1 - 131.2 (7.0)

Figure S6.  Get High-res Image Gene #28: '16p gain' versus Clinical Feature #1: 'Time to Death'

'17p gain' versus 'NUMBER.OF.LYMPH.NODES'

P value = 3.04e-06 (t-test), Q value = 0.0021

Table S7.  Gene #30: '17p gain' versus Clinical Feature #9: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 98 1.9 (3.8)
17P GAIN CNV 5 0.0 (0.0)
17P GAIN WILD-TYPE 93 2.0 (3.8)

Figure S7.  Get High-res Image Gene #30: '17p gain' versus Clinical Feature #9: 'NUMBER.OF.LYMPH.NODES'

'6p loss' versus 'KARNOFSKY.PERFORMANCE.SCORE'

P value = 6.63e-05 (t-test), Q value = 0.046

Table S8.  Gene #48: '6p loss' versus Clinical Feature #4: 'KARNOFSKY.PERFORMANCE.SCORE'

nPatients Mean (Std.Dev)
ALL 37 78.1 (16.3)
6P LOSS CNV 4 90.0 (0.0)
6P LOSS WILD-TYPE 33 76.7 (16.7)

Figure S8.  Get High-res Image Gene #48: '6p loss' versus Clinical Feature #4: 'KARNOFSKY.PERFORMANCE.SCORE'

'16q loss' versus 'TOBACCOSMOKINGHISTORYINDICATOR'

P value = 4.43e-05 (t-test), Q value = 0.031

Table S9.  Gene #64: '16q loss' versus Clinical Feature #6: 'TOBACCOSMOKINGHISTORYINDICATOR'

nPatients Mean (Std.Dev)
ALL 80 2.8 (1.2)
16Q LOSS CNV 11 3.6 (0.5)
16Q LOSS WILD-TYPE 69 2.7 (1.2)

Figure S9.  Get High-res Image Gene #64: '16q loss' versus Clinical Feature #6: 'TOBACCOSMOKINGHISTORYINDICATOR'

Methods & Data
Input

  • Mutation data file = broad_values_by_arm.mutsig.cluster.txt

  • Clinical data file = BLCA-TP.clin.merged.picked.txt

  • Number of patients = 131

  • Number of significantly arm-level cnvs = 74

  • Number of selected clinical features = 11

  • 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

Student's t-test analysis

For continuous numerical clinical features, two-tailed Student's t test with unequal variance (Lehmann and Romano 2005) was applied to compare the clinical values between tumors with and without gene mutations using 't.test' 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

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.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.

References
[1] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)
[2] Lehmann and Romano, Testing Statistical Hypotheses (3E ed.), New York: Springer. ISBN 0387988645 (2005)
[3] 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)
[4] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[5] 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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