Correlation between copy number variations of arm-level result and selected clinical features
Lung Adenocarcinoma (Primary solid tumor)
17 April 2019  |  None
Maintainer Information
Maintained by Broad Institute GDAC (Broad Institute of MIT & Harvard)
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 95 arm-level events and 17 clinical features across 110 patients, 23 significant findings detected with Q value < 0.25.

  • 5q gain cnv correlated to 'SMOKER'.

  • 14q gain cnv correlated to 'YEARS_TO_BIRTH'.

  • xp gain cnv correlated to 'ORIGIN_ASIA'.

  • 1p loss cnv correlated to 'YEARS_TO_BIRTH'.

  • 2p loss cnv correlated to 'PATHOLOGY_T_STAGE'.

  • 4q loss cnv correlated to 'BMI'.

  • 6p loss cnv correlated to 'YEARS_TO_BIRTH' and 'ORIGIN_ASIA'.

  • 13q loss cnv correlated to 'ORIGIN_ASIA'.

  • 14p loss cnv correlated to 'KARNOFSKY_PERFORMANCE_SCORE' and 'COUNTRY_OF_ORIGIN'.

  • 14q loss cnv correlated to 'COUNTRY_OF_ORIGIN'.

  • 19p loss cnv correlated to 'BMI'.

  • 21p loss cnv correlated to 'BMI'.

  • 21q loss cnv correlated to 'BMI'.

  • 22p loss cnv correlated to 'BMI',  'COUNTRY_OF_ORIGIN', and 'ORIGIN_ASIA'.

  • 22q loss cnv correlated to 'BMI',  'COUNTRY_OF_ORIGIN', and 'ORIGIN_ASIA'.

  • yp loss cnv correlated to 'PATHOLOGIC_STAGE'.

  • yq loss cnv correlated to 'PATHOLOGIC_STAGE'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 95 arm-level events and 17 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 23 significant findings detected.

Clinical
Features 		DAYS
TO
DEATH
OR
LAST
FUP 		HISTOLOGICAL
TYPE 		HISTOLOGIC
GRADE 		KARNOFSKY
PERFORMANCE
SCORE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGIC
STAGE 		YEARS
TO
BIRTH 		ETHNICITY GENDER RACE RADIATION
THERAPY 		BMI NUMBER
PACK
YEARS
SMOKED 		SMOKER COUNTRY
OF
ORIGIN 		ORIGIN
ASIA
nCNV (%) nWild-Type logrank test Fisher's exact test Fisher's exact test Wilcoxon-test Fisher's exact test Fisher's exact test Fisher's exact test Wilcoxon-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 Fisher's exact test
22p loss 47 (43%) 63 0.0414
(0.603) 		0.00722
(0.324) 		0.277
(0.874) 		0.415
(0.944) 		0.104
(0.723) 		1
(1.00) 		0.853
(1.00) 		0.518
(0.985) 		0.477
(0.963) 		0.00768
(0.335) 		1
(1.00) 		0.223
(0.833) 		0.00305
(0.244) 		0.287
(0.876) 		0.43
(0.952) 		0.00103
(0.202) 		0.000359
(0.193)
22q loss 49 (45%) 61 0.0562
(0.651) 		0.00454
(0.293) 		0.273
(0.869) 		0.3
(0.885) 		0.227
(0.833) 		0.774
(1.00) 		0.963
(1.00) 		0.288
(0.876) 		0.421
(0.944) 		0.00917
(0.365) 		1
(1.00) 		0.321
(0.896) 		0.00217
(0.244) 		0.234
(0.833) 		0.845
(1.00) 		0.00027
(0.193) 		8.9e-05
(0.144)
6p loss 19 (17%) 91 0.909
(1.00) 		0.684
(1.00) 		0.547
(0.994) 		0.356
(0.913) 		0.654
(1.00) 		0.0194
(0.475) 		0.017
(0.474) 		0.00101
(0.202) 		0.158
(0.78) 		0.792
(1.00) 		0.18
(0.794) 		0.415
(0.944) 		0.273
(0.869) 		0.0728
(0.677) 		0.375
(0.926) 		0.00206
(0.244)
14p loss 34 (31%) 76 0.66
(1.00) 		0.171
(0.793) 		0.81
(1.00) 		0.00257
(0.244) 		0.556
(0.994) 		0.865
(1.00) 		0.866
(1.00) 		0.0104
(0.389) 		1
(1.00) 		0.663
(1.00) 		1
(1.00) 		0.594
(1.00) 		0.566
(1.00) 		0.601
(1.00) 		1
(1.00) 		0.00332
(0.244) 		0.53
(0.99)
5q gain 26 (24%) 84 0.164
(0.78) 		0.707
(1.00) 		0.439
(0.956) 		0.76
(1.00) 		0.591
(1.00) 		0.0394
(0.594) 		0.67
(1.00) 		0.252
(0.837) 		0.477
(0.963) 		0.00437
(0.293) 		1
(1.00) 		0.404
(0.942) 		0.582
(1.00) 		0.417
(0.944) 		0.00113
(0.202) 		0.355
(0.913) 		0.0629
(0.668)
14q gain 27 (25%) 83 0.418
(0.944) 		0.231
(0.833) 		0.0997
(0.722) 		0.0727
(0.677) 		0.431
(0.952) 		0.251
(0.837) 		0.888
(1.00) 		0.00306
(0.244) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.404
(0.942) 		0.147
(0.778) 		0.405
(0.942) 		0.177
(0.794) 		0.597
(1.00) 		0.0112
(0.393)
xp gain 46 (42%) 64 0.194
(0.814) 		0.347
(0.91) 		0.207
(0.826) 		0.19
(0.808) 		0.477
(0.963) 		0.957
(1.00) 		0.739
(1.00) 		0.01
(0.386) 		0.241
(0.837) 		0.683
(1.00) 		1
(1.00) 		0.228
(0.833) 		0.28
(0.874) 		0.205
(0.824) 		0.24
(0.836) 		0.115
(0.735) 		0.00288
(0.244)
1p loss 16 (15%) 94 0.819
(1.00) 		0.461
(0.956) 		0.457
(0.956) 		0.0762
(0.678) 		0.00847
(0.36) 		0.779
(1.00) 		0.264
(0.859) 		0.00351
(0.246) 		0.23
(0.833) 		0.571
(1.00) 		0.469
(0.959) 		0.153
(0.78) 		0.0153
(0.458) 		1
(1.00) 		0.134
(0.771) 		0.176
(0.794)
2p loss 8 (7%) 102 0.401
(0.941) 		0.727
(1.00) 		0.64
(1.00) 		0.354
(0.913) 		0.00274
(0.244) 		1
(1.00) 		0.0901
(0.704) 		0.557
(0.994) 		1
(1.00) 		0.438
(0.956) 		1
(1.00) 		0.754
(1.00) 		0.285
(0.876) 		0.89
(1.00) 		0.465
(0.959)
4q loss 19 (17%) 91 0.485
(0.97) 		0.852
(1.00) 		0.154
(0.78) 		0.0134
(0.441) 		0.333
(0.898) 		0.444
(0.956) 		0.404
(0.942) 		0.828
(1.00) 		1
(1.00) 		0.596
(1.00) 		0.306
(0.89) 		0.355
(0.913) 		0.00176
(0.237) 		0.164
(0.78) 		0.799
(1.00) 		0.0592
(0.651) 		0.0739
(0.677)
13q loss 48 (44%) 62 0.698
(1.00) 		0.786
(1.00) 		0.0746
(0.677) 		0.162
(0.78) 		1
(1.00) 		0.0785
(0.678) 		0.493
(0.971) 		0.445
(0.956) 		1
(1.00) 		0.542
(0.994) 		1
(1.00) 		0.146
(0.778) 		0.38
(0.926) 		0.161
(0.78) 		0.239
(0.836) 		0.0197
(0.475) 		0.0033
(0.244)
14q loss 10 (9%) 100 0.663
(1.00) 		0.261
(0.854) 		0.283
(0.876) 		0.0144
(0.446) 		0.173
(0.794) 		0.689
(1.00) 		0.52
(0.985) 		0.495
(0.972) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.42
(0.944) 		0.0668
(0.67) 		0.285
(0.876) 		0.00276
(0.244) 		0.739
(1.00)
19p loss 45 (41%) 65 0.292
(0.88) 		0.32
(0.896) 		0.651
(1.00) 		0.312
(0.89) 		0.523
(0.985) 		0.918
(1.00) 		0.641
(1.00) 		0.378
(0.926) 		1
(1.00) 		0.838
(1.00) 		0.293
(0.88) 		0.613
(1.00) 		0.00068
(0.202) 		0.452
(0.956) 		0.691
(1.00) 		0.715
(1.00) 		0.692
(1.00)
21p loss 42 (38%) 68 0.843
(1.00) 		0.649
(1.00) 		0.702
(1.00) 		0.0653
(0.67) 		0.0612
(0.655) 		0.702
(1.00) 		0.187
(0.803) 		0.698
(1.00) 		1
(1.00) 		0.218
(0.833) 		1
(1.00) 		0.613
(1.00) 		0.00151
(0.222) 		0.0371
(0.58) 		0.314
(0.89) 		0.0441
(0.604) 		0.0767
(0.678)
21q loss 38 (35%) 72 0.538
(0.994) 		0.883
(1.00) 		0.717
(1.00) 		0.081
(0.678) 		0.106
(0.723) 		0.629
(1.00) 		0.138
(0.771) 		0.912
(1.00) 		1
(1.00) 		0.291
(0.879) 		1
(1.00) 		0.795
(1.00) 		0.00138
(0.222) 		0.0471
(0.633) 		0.31
(0.89) 		0.0463
(0.628) 		0.153
(0.78)
yp loss 63 (57%) 47 0.731
(1.00) 		0.122
(0.739) 		0.152
(0.78) 		0.196
(0.814) 		0.308
(0.89) 		0.181
(0.794) 		0.00083
(0.202) 		0.657
(1.00) 		1
(1.00) 		0.105
(0.723) 		0.815
(1.00) 		0.806
(1.00) 		0.86
(1.00) 		0.579
(1.00) 		0.557
(0.994) 		0.207
(0.826) 		0.846
(1.00)
yq loss 64 (58%) 46 0.738
(1.00) 		0.0571
(0.651) 		0.156
(0.78) 		0.163
(0.78) 		0.422
(0.944) 		0.158
(0.78) 		0.00075
(0.202) 		0.983
(1.00) 		1
(1.00) 		0.315
(0.89) 		0.839
(1.00) 		1
(1.00) 		0.995
(1.00) 		0.726
(1.00) 		1
(1.00) 		0.0978
(0.714) 		1
(1.00)
1p gain 32 (29%) 78 0.27
(0.866) 		0.279
(0.874) 		0.0439
(0.604) 		0.55
(0.994) 		0.314
(0.89) 		0.163
(0.78) 		0.211
(0.833) 		0.0143
(0.446) 		1
(1.00) 		0.0266
(0.517) 		0.751
(1.00) 		0.595
(1.00) 		0.336
(0.898) 		0.417
(0.944) 		0.672
(1.00) 		0.648
(1.00) 		0.289
(0.877)
1q gain 66 (60%) 44 0.223
(0.833) 		0.239
(0.836) 		0.599
(1.00) 		0.555
(0.994) 		0.46
(0.956) 		0.8
(1.00) 		0.938
(1.00) 		0.617
(1.00) 		0.554
(0.994) 		0.15
(0.78) 		0.33
(0.898) 		0.8
(1.00) 		0.563
(0.999) 		0.217
(0.833) 		1
(1.00) 		0.684
(1.00) 		0.23
(0.833)
2p gain 23 (21%) 87 0.154
(0.78) 		0.832
(1.00) 		0.716
(1.00) 		0.763
(1.00) 		0.607
(1.00) 		0.5
(0.975) 		0.425
(0.947) 		0.895
(1.00) 		1
(1.00) 		0.219
(0.833) 		1
(1.00) 		0.389
(0.929) 		0.65
(1.00) 		0.587
(1.00) 		0.477
(0.963) 		0.544
(0.994) 		0.809
(1.00)
2q gain 21 (19%) 89 0.229
(0.833) 		0.939
(1.00) 		0.777
(1.00) 		0.799
(1.00) 		0.451
(0.956) 		0.583
(1.00) 		0.458
(0.956) 		0.921
(1.00) 		1
(1.00) 		0.441
(0.956) 		1
(1.00) 		0.235
(0.833) 		0.709
(1.00) 		0.244
(0.837) 		0.806
(1.00) 		0.501
(0.975) 		0.804
(1.00)
3p gain 10 (9%) 100 0.902
(1.00) 		0.582
(1.00) 		0.466
(0.959) 		0.0254
(0.517) 		0.626
(1.00) 		0.214
(0.833) 		0.588
(1.00) 		0.305
(0.89) 		1
(1.00) 		0.49
(0.97) 		0.0865
(0.688) 		0.395
(0.937) 		0.464
(0.959) 		0.742
(1.00) 		0.258
(0.848) 		0.0432
(0.604)
3q gain 18 (16%) 92 0.557
(0.994) 		0.382
(0.927) 		0.808
(1.00) 		0.0528
(0.651) 		0.37
(0.922) 		0.117
(0.737) 		0.493
(0.972) 		0.228
(0.833) 		1
(1.00) 		0.413
(0.944) 		1
(1.00) 		0.0318
(0.554) 		0.255
(0.839) 		0.436
(0.956) 		0.604
(1.00) 		0.25
(0.837) 		0.0199
(0.475)
4p gain 8 (7%) 102 0.581
(1.00) 		0.544
(0.994) 		0.12
(0.737) 		0.0604
(0.651) 		0.264
(0.859) 		1
(1.00) 		0.21
(0.833) 		0.545
(0.994) 		1
(1.00) 		0.438
(0.956) 		1
(1.00) 		0.251
(0.837) 		0.985
(1.00) 		1
(1.00) 		0.0931
(0.712) 		0.465
(0.959)
4q gain 7 (6%) 103 0.638
(1.00) 		0.516
(0.985) 		0.195
(0.814) 		0.0575
(0.651) 		0.141
(0.771) 		0.729
(1.00) 		0.0377
(0.58) 		0.394
(0.937) 		1
(1.00) 		0.222
(0.833) 		1
(1.00) 		0.295
(0.885) 		0.597
(1.00) 		1
(1.00) 		0.0964
(0.714) 		0.235
(0.833)
5p gain 57 (52%) 53 0.715
(1.00) 		0.593
(1.00) 		0.459
(0.956) 		0.623
(1.00) 		0.49
(0.97) 		0.0684
(0.672) 		0.861
(1.00) 		0.443
(0.956) 		1
(1.00) 		0.314
(0.89) 		0.46
(0.956) 		1
(1.00) 		0.0864
(0.688) 		0.428
(0.952) 		0.558
(0.994) 		0.0529
(0.651) 		0.0313
(0.554)
6p gain 20 (18%) 90 0.416
(0.944) 		0.95
(1.00) 		0.75
(1.00) 		0.711
(1.00) 		0.762
(1.00) 		0.242
(0.837) 		0.111
(0.723) 		0.548
(0.994) 		1
(1.00) 		0.798
(1.00) 		1
(1.00) 		0.754
(1.00) 		0.826
(1.00) 		0.917
(1.00) 		0.617
(1.00) 		0.518
(0.985) 		1
(1.00)
6q gain 10 (9%) 100 0.234
(0.833) 		0.914
(1.00) 		0.933
(1.00) 		0.701
(1.00) 		0.882
(1.00) 		0.379
(0.926) 		0.364
(0.916) 		0.934
(1.00) 		1
(1.00) 		0.49
(0.97) 		1
(1.00) 		0.442
(0.956) 		0.123
(0.739) 		0.912
(1.00) 		0.51
(0.983) 		0.198
(0.818) 		0.314
(0.89)
7p gain 58 (53%) 52 0.538
(0.994) 		0.0596
(0.651) 		0.144
(0.778) 		0.509
(0.983) 		0.512
(0.985) 		0.0725
(0.677) 		0.0711
(0.677) 		0.318
(0.896) 		0.275
(0.872) 		1
(1.00) 		1
(1.00) 		0.626
(1.00) 		0.69
(1.00) 		0.123
(0.739) 		0.848
(1.00) 		0.0299
(0.543) 		0.0194
(0.475)
7q gain 48 (44%) 62 0.66
(1.00) 		0.148
(0.779) 		0.018
(0.475) 		0.379
(0.926) 		0.629
(1.00) 		0.057
(0.651) 		0.877
(1.00) 		0.225
(0.833) 		0.548
(0.994) 		0.688
(1.00) 		1
(1.00) 		0.807
(1.00) 		0.45
(0.956) 		0.708
(1.00) 		0.557
(0.994) 		0.0111
(0.393) 		0.00659
(0.304)
8p gain 20 (18%) 90 0.369
(0.922) 		0.366
(0.917) 		0.194
(0.814) 		0.619
(1.00) 		0.298
(0.885) 		0.66
(1.00) 		0.768
(1.00) 		0.525
(0.985) 		0.362
(0.913) 		0.196
(0.814) 		1
(1.00) 		0.196
(0.814) 		0.971
(1.00) 		0.855
(1.00) 		1
(1.00) 		0.421
(0.944) 		0.2
(0.818)
8q gain 34 (31%) 76 0.435
(0.956) 		0.147
(0.778) 		0.459
(0.956) 		0.872
(1.00) 		0.32
(0.896) 		1
(1.00) 		0.884
(1.00) 		0.234
(0.833) 		1
(1.00) 		1
(1.00) 		0.543
(0.994) 		0.0175
(0.475) 		0.0906
(0.704) 		0.724
(1.00) 		0.832
(1.00) 		0.452
(0.956) 		0.032
(0.554)
9p gain 7 (6%) 103 0.361
(0.913) 		0.861
(1.00) 		0.878
(1.00) 		0.154
(0.78) 		0.733
(1.00) 		0.838
(1.00) 		0.981
(1.00) 		0.388
(0.929) 		1
(1.00) 		0.0929
(0.712) 		0.667
(1.00) 		0.682
(1.00) 		0.777
(1.00) 		0.46
(0.956) 		0.745
(1.00) 		0.235
(0.833)
9q gain 5 (5%) 105 0.388
(0.929) 		0.558
(0.994) 		0.828
(1.00) 		0.351
(0.912) 		0.798
(1.00) 		1
(1.00) 		0.847
(1.00) 		0.413
(0.944) 		1
(1.00) 		0.166
(0.78) 		0.589
(1.00) 		0.392
(0.933) 		0.65
(1.00) 		0.915
(1.00) 		0.399
(0.939)
10p gain 15 (14%) 95 0.135
(0.771) 		0.381
(0.926) 		0.759
(1.00) 		0.317
(0.895) 		0.217
(0.833) 		0.337
(0.898) 		0.298
(0.885) 		0.214
(0.833) 		1
(1.00) 		0.77
(1.00) 		1
(1.00) 		0.725
(1.00) 		0.396
(0.937) 		0.609
(1.00) 		0.576
(1.00) 		0.612
(1.00) 		0.147
(0.778)
10q gain 7 (6%) 103 0.829
(1.00) 		0.537
(0.994) 		0.88
(1.00) 		0.667
(1.00) 		0.339
(0.901) 		0.223
(0.833) 		0.134
(0.771) 		0.213
(0.833) 		1
(1.00) 		0.686
(1.00) 		1
(1.00) 		0.404
(0.942) 		0.0855
(0.688) 		1
(1.00) 		0.744
(1.00) 		0.235
(0.833)
11p gain 21 (19%) 89 0.336
(0.898) 		0.188
(0.806) 		0.171
(0.793) 		0.829
(1.00) 		1
(1.00) 		0.153
(0.78) 		0.33
(0.898) 		0.503
(0.979) 		0.477
(0.963) 		0.0701
(0.677) 		1
(1.00) 		0.235
(0.833) 		0.0665
(0.67) 		0.62
(1.00) 		0.00592
(0.304) 		0.954
(1.00) 		0.808
(1.00)
11q gain 24 (22%) 86 0.253
(0.837) 		0.578
(1.00) 		0.179
(0.794) 		0.614
(1.00) 		0.833
(1.00) 		0.328
(0.898) 		0.902
(1.00) 		0.48
(0.964) 		1
(1.00) 		0.221
(0.833) 		1
(1.00) 		1
(1.00) 		0.12
(0.737) 		0.897
(1.00) 		0.349
(0.912) 		0.974
(1.00) 		1
(1.00)
12p gain 23 (21%) 87 0.186
(0.803) 		0.697
(1.00) 		0.18
(0.794) 		0.141
(0.771) 		0.154
(0.78) 		0.297
(0.885) 		0.801
(1.00) 		0.46
(0.956) 		1
(1.00) 		0.219
(0.833) 		1
(1.00) 		0.758
(1.00) 		0.253
(0.837) 		0.705
(1.00) 		0.159
(0.78) 		0.647
(1.00) 		0.0334
(0.562)
12q gain 22 (20%) 88 0.214
(0.833) 		0.688
(1.00) 		0.186
(0.803) 		0.143
(0.776) 		0.0655
(0.67) 		0.216
(0.833) 		0.476
(0.963) 		0.673
(1.00) 		1
(1.00) 		0.129
(0.758) 		1
(1.00) 		0.539
(0.994) 		0.369
(0.922) 		0.577
(1.00) 		0.0972
(0.714) 		0.604
(1.00) 		0.0538
(0.651)
13p gain 7 (6%) 103 0.516
(0.985) 		0.834
(1.00) 		0.468
(0.959) 		0.783
(1.00) 		1
(1.00) 		0.467
(0.959) 		0.331
(0.898) 		0.637
(1.00) 		0.298
(0.885) 		1
(1.00) 		0.236
(0.835) 		0.33
(0.898) 		0.745
(1.00) 		0.0726
(0.677) 		0.46
(0.956) 		0.506
(0.982) 		0.692
(1.00)
13q gain 4 (4%) 106 0.589
(1.00) 		0.497
(0.973) 		0.599
(1.00) 		0.582
(1.00) 		1
(1.00) 		0.0575
(0.651) 		0.581
(1.00) 		1
(1.00) 		1
(1.00) 		0.238
(0.836) 		0.569
(1.00) 		0.778
(1.00) 		1
(1.00) 		0.436
(0.956) 		0.57
(1.00)
14p gain 26 (24%) 84 0.322
(0.896) 		0.787
(1.00) 		0.44
(0.956) 		0.108
(0.723) 		0.499
(0.975) 		0.18
(0.794) 		0.843
(1.00) 		0.0474
(0.633) 		0.477
(0.963) 		1
(1.00) 		1
(1.00) 		0.567
(1.00) 		0.583
(1.00) 		0.598
(1.00) 		0.111
(0.723) 		0.713
(1.00) 		0.165
(0.78)
15p gain 9 (8%) 101 0.955
(1.00) 		1
(1.00) 		0.078
(0.678) 		0.49
(0.97) 		0.772
(1.00) 		0.202
(0.821) 		0.266
(0.862) 		0.268
(0.864) 		0.0811
(0.678) 		0.268
(0.864) 		0.667
(1.00) 		0.811
(1.00) 		0.238
(0.836) 		1
(1.00) 		0.0795
(0.678) 		0.3
(0.885)
16p gain 37 (34%) 73 0.194
(0.814) 		0.357
(0.913) 		0.607
(1.00) 		0.347
(0.91) 		0.722
(1.00) 		0.0413
(0.603) 		0.0257
(0.517) 		0.0687
(0.672) 		0.141
(0.771) 		0.0206
(0.475) 		1
(1.00) 		0.2
(0.818) 		0.302
(0.89) 		0.279
(0.874) 		0.0064
(0.304) 		0.0562
(0.651) 		0.0391
(0.594)
16q gain 28 (25%) 82 0.452
(0.956) 		0.58
(1.00) 		0.322
(0.896) 		0.315
(0.89) 		0.3
(0.885) 		0.0783
(0.678) 		0.106
(0.723) 		0.0951
(0.714) 		0.0856
(0.688) 		0.0192
(0.475) 		1
(1.00) 		0.264
(0.859) 		0.404
(0.942) 		0.519
(0.985) 		0.111
(0.723) 		0.101
(0.723) 		0.122
(0.739)
17p gain 22 (20%) 88 0.288
(0.876) 		0.757
(1.00) 		0.738
(1.00) 		0.546
(0.994) 		0.351
(0.912) 		0.0278
(0.528) 		0.253
(0.837) 		0.496
(0.972) 		1
(1.00) 		0.803
(1.00) 		1
(1.00) 		0.221
(0.833) 		0.707
(1.00) 		0.787
(1.00) 		0.813
(1.00) 		0.951
(1.00) 		0.808
(1.00)
17q gain 30 (27%) 80 0.401
(0.941) 		0.637
(1.00) 		0.447
(0.956) 		0.359
(0.913) 		0.269
(0.864) 		0.0374
(0.58) 		0.541
(0.994) 		0.83
(1.00) 		1
(1.00) 		0.658
(1.00) 		1
(1.00) 		0.165
(0.78) 		0.923
(1.00) 		0.641
(1.00) 		1
(1.00) 		0.716
(1.00) 		0.388
(0.929)
18p gain 8 (7%) 102 0.726
(1.00) 		0.896
(1.00) 		0.748
(1.00) 		0.69
(1.00) 		0.103
(0.723) 		1
(1.00) 		0.62
(1.00) 		0.12
(0.737) 		0.715
(1.00) 		1
(1.00) 		0.585
(1.00) 		0.985
(1.00) 		0.46
(0.956) 		0.177
(0.794) 		0.136
(0.771)
18q gain 7 (6%) 103 0.718
(1.00) 		0.862
(1.00) 		0.635
(1.00) 		0.635
(1.00) 		0.28
(0.874) 		0.731
(1.00) 		0.517
(0.985) 		0.0051
(0.293) 		1
(1.00) 		0.624
(1.00) 		1
(1.00) 		0.335
(0.898) 		0.46
(0.956) 		0.232
(0.833) 		0.235
(0.833)
19p gain 14 (13%) 96 0.556
(0.994) 		0.277
(0.874) 		0.251
(0.837) 		0.592
(1.00) 		0.917
(1.00) 		0.76
(1.00) 		0.982
(1.00) 		0.716
(1.00) 		1
(1.00) 		0.134
(0.771) 		1
(1.00) 		1
(1.00) 		0.979
(1.00) 		0.827
(1.00) 		0.578
(1.00) 		0.749
(1.00) 		1
(1.00)
19q gain 15 (14%) 95 0.515
(0.985) 		0.33
(0.898) 		0.869
(1.00) 		0.331
(0.898) 		0.701
(1.00) 		0.18
(0.794) 		0.952
(1.00) 		0.553
(0.994) 		1
(1.00) 		0.0851
(0.688) 		1
(1.00) 		0.734
(1.00) 		0.859
(1.00) 		0.954
(1.00) 		1
(1.00) 		0.745
(1.00) 		1
(1.00)
20p gain 24 (22%) 86 0.201
(0.818) 		0.439
(0.956) 		0.365
(0.916) 		0.00526
(0.293) 		0.29
(0.877) 		0.61
(1.00) 		0.535
(0.994) 		0.079
(0.678) 		1
(1.00) 		0.807
(1.00) 		1
(1.00) 		0.787
(1.00) 		0.56
(0.997) 		0.0738
(0.677) 		1
(1.00) 		0.0561
(0.651) 		0.815
(1.00)
20q gain 29 (26%) 81 0.109
(0.723) 		0.832
(1.00) 		0.173
(0.794) 		0.0322
(0.554) 		0.593
(1.00) 		0.336
(0.898) 		0.23
(0.833) 		0.0191
(0.475) 		1
(1.00) 		0.821
(1.00) 		1
(1.00) 		0.595
(1.00) 		0.72
(1.00) 		0.273
(0.869) 		0.825
(1.00) 		0.0493
(0.647) 		0.51
(0.983)
21p gain 4 (4%) 106 0.298
(0.885) 		0.139
(0.771) 		0.0772
(0.678) 		1
(1.00) 		0.253
(0.837) 		0.122
(0.739) 		0.603
(1.00) 		1
(1.00) 		0.0114
(0.393) 		0.235
(0.833) 		1
(1.00) 		0.407
(0.944) 		0.312
(0.89) 		0.71
(1.00) 		0.57
(1.00)
21q gain 16 (15%) 94 0.61
(1.00) 		0.945
(1.00) 		0.233
(0.833) 		0.331
(0.898) 		0.922
(1.00) 		0.767
(1.00) 		0.683
(1.00) 		0.0308
(0.553) 		1
(1.00) 		0.397
(0.938) 		0.431
(0.952) 		0.734
(1.00) 		0.325
(0.898) 		0.526
(0.986) 		0.591
(1.00) 		0.99
(1.00) 		0.579
(1.00)
22p gain 4 (4%) 106 0.495
(0.972) 		0.858
(1.00) 		0.0778
(0.678) 		0.112
(0.723) 		0.591
(1.00) 		0.18
(0.794) 		0.354
(0.913) 		1
(1.00) 		0.11
(0.723) 		1
(1.00) 		0.164
(0.78) 		0.312
(0.89) 		0.189
(0.808) 		0.306
(0.89)
22q gain 3 (3%) 107 0.764
(1.00) 		0.0501
(0.651) 		0.299
(0.885) 		0.465
(0.959) 		0.248
(0.837) 		0.551
(0.994) 		1
(1.00) 		0.036
(0.576) 		1
(1.00) 		0.408
(0.944) 		0.576
(1.00) 		0.438
(0.956) 		0.57
(1.00)
xq gain 49 (45%) 61 0.141
(0.771) 		0.149
(0.779) 		0.412
(0.944) 		0.646
(1.00) 		0.884
(1.00) 		0.841
(1.00) 		0.575
(1.00) 		0.0413
(0.603) 		0.205
(0.825) 		0.417
(0.944) 		1
(1.00) 		0.337
(0.898) 		0.213
(0.833) 		0.457
(0.956) 		0.17
(0.792) 		0.0744
(0.677) 		0.00659
(0.304)
yp gain 24 (22%) 86 0.561
(0.997) 		0.523
(0.985) 		0.131
(0.764) 		0.608
(1.00) 		0.456
(0.956) 		0.0228
(0.502) 		0.0441
(0.604) 		0.868
(1.00) 		1
(1.00) 		0.221
(0.833) 		0.543
(0.994) 		0.235
(0.833) 		0.119
(0.737) 		0.119
(0.737) 		0.478
(0.963) 		0.635
(1.00) 		0.815
(1.00)
yq gain 17 (15%) 93 0.579
(1.00) 		0.166
(0.781) 		0.264
(0.859) 		0.0355
(0.576) 		0.491
(0.97) 		0.67
(1.00) 		0.467
(0.959) 		0.513
(0.985) 		0.477
(0.963) 		0.578
(1.00) 		0.43
(0.952) 		0.748
(1.00) 		0.128
(0.758) 		0.938
(1.00) 		0.412
(0.944) 		0.103
(0.723) 		1
(1.00)
1q loss 6 (5%) 104 0.0972
(0.714) 		0.466
(0.959) 		0.733
(1.00) 		0.137
(0.771) 		0.0161
(0.464) 		1
(1.00) 		0.381
(0.926) 		0.105
(0.723) 		0.0811
(0.678) 		0.662
(1.00) 		1
(1.00) 		0.326
(0.898) 		0.0344
(0.572) 		0.698
(1.00) 		0.651
(1.00) 		0.397
(0.938)
2q loss 10 (9%) 100 0.308
(0.89) 		0.311
(0.89) 		0.634
(1.00) 		0.341
(0.901) 		0.0376
(0.58) 		0.89
(1.00) 		0.252
(0.837) 		0.64
(1.00) 		1
(1.00) 		0.73
(1.00) 		1
(1.00) 		0.659
(1.00) 		0.0957
(0.714) 		0.816
(1.00) 		0.189
(0.808)
3p loss 36 (33%) 74 0.252
(0.837) 		0.853
(1.00) 		0.0581
(0.651) 		0.544
(0.994) 		0.0359
(0.576) 		0.752
(1.00) 		0.286
(0.876) 		0.138
(0.771) 		1
(1.00) 		0.398
(0.938) 		0.717
(1.00) 		1
(1.00) 		0.164
(0.78) 		0.508
(0.983) 		0.543
(0.994) 		0.926
(1.00) 		0.539
(0.994)
3q loss 27 (25%) 83 0.179
(0.794) 		0.897
(1.00) 		0.303
(0.89) 		0.349
(0.912) 		0.178
(0.794) 		0.319
(0.896) 		0.0886
(0.698) 		0.0141
(0.446) 		1
(1.00) 		0.36
(0.913) 		0.542
(0.994) 		0.775
(1.00) 		0.0483
(0.64) 		0.137
(0.771) 		0.654
(1.00) 		0.997
(1.00) 		0.655
(1.00)
4p loss 19 (17%) 91 0.916
(1.00) 		0.85
(1.00) 		0.157
(0.78) 		0.00478
(0.293) 		0.808
(1.00) 		0.288
(0.876) 		0.319
(0.896) 		0.553
(0.994) 		1
(1.00) 		0.287
(0.876) 		1
(1.00) 		0.355
(0.913) 		0.00898
(0.365) 		0.41
(0.944) 		0.799
(1.00) 		0.287
(0.876) 		0.0739
(0.677)
5p loss 7 (6%) 103 0.0601
(0.651) 		0.0961
(0.714) 		0.384
(0.929) 		0.947
(1.00) 		0.733
(1.00) 		0.838
(1.00) 		1
(1.00) 		0.602
(1.00) 		0.42
(0.944) 		0.589
(1.00) 		0.616
(1.00) 		0.0822
(0.684) 		0.113
(0.723) 		0.697
(1.00)
5q loss 19 (17%) 91 0.379
(0.926) 		0.139
(0.771) 		0.836
(1.00) 		0.157
(0.78) 		0.864
(1.00) 		0.245
(0.837) 		0.359
(0.913) 		0.42
(0.944) 		1
(1.00) 		0.108
(0.723) 		1
(1.00) 		0.748
(1.00) 		0.797
(1.00) 		0.407
(0.944) 		0.604
(1.00) 		0.101
(0.723) 		0.444
(0.956)
6q loss 31 (28%) 79 0.486
(0.97) 		0.921
(1.00) 		0.747
(1.00) 		0.412
(0.944) 		1
(1.00) 		0.206
(0.826) 		0.17
(0.792) 		0.00496
(0.293) 		0.0856
(0.688) 		0.122
(0.739) 		1
(1.00) 		0.165
(0.78) 		0.213
(0.833) 		0.204
(0.824) 		0.0542
(0.651) 		0.518
(0.985) 		0.0513
(0.651)
7p loss 8 (7%) 102 0.326
(0.898) 		0.695
(1.00) 		0.379
(0.926) 		0.895
(1.00) 		0.865
(1.00) 		0.481
(0.964) 		0.552
(0.994) 		0.201
(0.818) 		1
(1.00) 		0.0168
(0.474) 		0.142
(0.771) 		0.385
(0.929) 		0.723
(1.00) 		0.506
(0.982) 		0.717
(1.00)
7q loss 9 (8%) 101 0.335
(0.898) 		0.516
(0.985) 		0.342
(0.901) 		0.811
(1.00) 		0.773
(1.00) 		1
(1.00) 		0.915
(1.00) 		0.0982
(0.714) 		1
(1.00) 		0.00646
(0.304) 		1
(1.00) 		0.667
(1.00) 		0.21
(0.833) 		0.137
(0.771) 		0.729
(1.00) 		0.35
(0.912) 		0.16
(0.78)
8p loss 33 (30%) 77 0.193
(0.814) 		0.313
(0.89) 		0.129
(0.758) 		0.933
(1.00) 		0.375
(0.926) 		0.359
(0.913) 		0.931
(1.00) 		0.581
(1.00) 		1
(1.00) 		0.509
(0.983) 		0.542
(0.994) 		1
(1.00) 		0.0525
(0.651) 		0.112
(0.723) 		0.139
(0.771) 		0.799
(1.00) 		0.0872
(0.69)
8q loss 15 (14%) 95 0.176
(0.794) 		0.586
(1.00) 		0.755
(1.00) 		0.496
(0.972) 		0.109
(0.723) 		0.278
(0.874) 		0.742
(1.00) 		0.927
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.148
(0.779) 		0.0114
(0.393) 		0.0218
(0.49) 		0.609
(1.00) 		0.0911
(0.704)
9p loss 53 (48%) 57 0.0792
(0.678) 		0.959
(1.00) 		0.48
(0.964) 		0.552
(0.994) 		0.491
(0.97) 		0.18
(0.794) 		0.295
(0.885) 		0.066
(0.67) 		1
(1.00) 		0.0158
(0.463) 		0.331
(0.898) 		0.0269
(0.517) 		0.184
(0.803) 		0.103
(0.723) 		0.247
(0.837) 		0.172
(0.794) 		0.0326
(0.554)
9q loss 54 (49%) 56 0.0979
(0.714) 		0.793
(1.00) 		0.458
(0.956) 		0.358
(0.913) 		0.241
(0.837) 		0.234
(0.833) 		0.0675
(0.672) 		0.152
(0.78) 		1
(1.00) 		0.0261
(0.517) 		0.331
(0.898) 		0.0298
(0.543) 		0.0267
(0.517) 		0.029
(0.543) 		0.333
(0.898) 		0.113
(0.723) 		0.0203
(0.475)
10p loss 26 (24%) 84 0.803
(1.00) 		0.666
(1.00) 		0.113
(0.723) 		0.661
(1.00) 		0.0591
(0.651) 		0.796
(1.00) 		0.124
(0.744) 		0.128
(0.758) 		0.362
(0.913) 		0.155
(0.78) 		0.305
(0.89) 		0.772
(1.00) 		0.163
(0.78) 		0.913
(1.00) 		0.0209
(0.475) 		0.523
(0.985) 		0.11
(0.723)
10q loss 28 (25%) 82 0.238
(0.836) 		0.371
(0.923) 		0.0555
(0.651) 		0.651
(1.00) 		0.12
(0.737) 		0.611
(1.00) 		0.083
(0.687) 		0.199
(0.818) 		0.477
(0.963) 		0.0398
(0.596) 		0.431
(0.952) 		0.574
(1.00) 		0.0972
(0.714) 		0.796
(1.00) 		0.177
(0.794) 		0.674
(1.00) 		0.271
(0.868)
11p loss 27 (25%) 83 0.793
(1.00) 		0.133
(0.771) 		0.192
(0.814) 		0.617
(1.00) 		0.72
(1.00) 		0.799
(1.00) 		0.93
(1.00) 		0.156
(0.78) 		1
(1.00) 		0.36
(0.913) 		1
(1.00) 		0.567
(1.00) 		0.186
(0.803) 		0.306
(0.89) 		0.654
(1.00) 		0.102
(0.723) 		0.0238
(0.503)
11q loss 22 (20%) 88 0.993
(1.00) 		0.7
(1.00) 		0.371
(0.923) 		0.75
(1.00) 		0.723
(1.00) 		0.769
(1.00) 		0.97
(1.00) 		0.147
(0.778) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.758
(1.00) 		0.417
(0.944) 		0.621
(1.00) 		0.813
(1.00) 		0.632
(1.00) 		0.0538
(0.651)
12p loss 24 (22%) 86 0.376
(0.926) 		0.638
(1.00) 		0.147
(0.778) 		0.793
(1.00) 		0.487
(0.97) 		0.835
(1.00) 		0.524
(0.985) 		0.476
(0.963) 		0.141
(0.771) 		0.221
(0.833) 		1
(1.00) 		0.767
(1.00) 		0.0707
(0.677) 		0.396
(0.937) 		1
(1.00) 		0.598
(1.00) 		1
(1.00)
12q loss 23 (21%) 87 0.387
(0.929) 		0.871
(1.00) 		0.45
(0.956) 		0.525
(0.985) 		0.445
(0.956) 		0.881
(1.00) 		0.332
(0.898) 		0.732
(1.00) 		0.112
(0.723) 		0.322
(0.896) 		1
(1.00) 		0.767
(1.00) 		0.158
(0.78) 		0.385
(0.929) 		0.813
(1.00) 		0.406
(0.944) 		1
(1.00)
13p loss 50 (45%) 60 0.526
(0.986) 		0.674
(1.00) 		0.57
(1.00) 		0.805
(1.00) 		0.813
(1.00) 		0.0684
(0.672) 		0.893
(1.00) 		0.712
(1.00) 		1
(1.00) 		0.421
(0.944) 		1
(1.00) 		0.631
(1.00) 		0.962
(1.00) 		0.244
(0.837) 		0.433
(0.953) 		0.488
(0.97) 		0.117
(0.737)
15p loss 58 (53%) 52 0.965
(1.00) 		0.457
(0.956) 		0.186
(0.803) 		0.46
(0.956) 		0.557
(0.994) 		0.811
(1.00) 		0.5
(0.975) 		0.265
(0.859) 		1
(1.00) 		0.0425
(0.604) 		1
(1.00) 		0.149
(0.779) 		0.971
(1.00) 		0.937
(1.00) 		0.117
(0.737) 		0.691
(1.00) 		0.698
(1.00)
15q loss 52 (47%) 58 0.389
(0.929) 		0.707
(1.00) 		0.361
(0.913) 		0.0649
(0.67) 		0.748
(1.00) 		0.534
(0.994) 		0.472
(0.963) 		0.976
(1.00) 		1
(1.00) 		0.0737
(0.677) 		1
(1.00) 		0.471
(0.963) 		0.375
(0.926) 		0.683
(1.00) 		0.0202
(0.475) 		0.333
(0.898) 		0.0808
(0.678)
16p loss 15 (14%) 95 0.246
(0.837) 		0.172
(0.794) 		0.667
(1.00) 		0.231
(0.833) 		0.414
(0.944) 		0.647
(1.00) 		0.252
(0.837) 		0.346
(0.91) 		1
(1.00) 		0.77
(1.00) 		1
(1.00) 		0.469
(0.959) 		0.252
(0.837) 		0.593
(1.00) 		1
(1.00) 		0.6
(1.00) 		0.0911
(0.704)
16q loss 24 (22%) 86 0.0939
(0.714) 		0.61
(1.00) 		0.452
(0.956) 		0.325
(0.898) 		0.227
(0.833) 		0.423
(0.945) 		0.275
(0.872) 		0.289
(0.876) 		1
(1.00) 		0.342
(0.901) 		1
(1.00) 		0.235
(0.833) 		0.185
(0.803) 		0.43
(0.952) 		0.817
(1.00) 		0.776
(1.00) 		0.0659
(0.67)
17p loss 24 (22%) 86 0.735
(1.00) 		0.109
(0.723) 		0.36
(0.913) 		0.899
(1.00) 		0.943
(1.00) 		1
(1.00) 		0.538
(0.994) 		0.13
(0.761) 		0.421
(0.944) 		0.221
(0.833) 		1
(1.00) 		0.382
(0.927) 		0.306
(0.89) 		0.313
(0.89) 		0.64
(1.00) 		0.65
(1.00) 		0.482
(0.966)
17q loss 18 (16%) 92 0.453
(0.956) 		0.129
(0.758) 		0.364
(0.916) 		0.743
(1.00) 		0.749
(1.00) 		0.861
(1.00) 		0.366
(0.917) 		0.203
(0.821) 		0.421
(0.944) 		0.0535
(0.651) 		1
(1.00) 		0.106
(0.723) 		0.287
(0.876) 		0.255
(0.839) 		0.792
(1.00) 		0.568
(1.00) 		0.799
(1.00)
18p loss 40 (36%) 70 0.82
(1.00) 		0.631
(1.00) 		0.827
(1.00) 		0.0802
(0.678) 		0.387
(0.929) 		0.794
(1.00) 		0.641
(1.00) 		0.024
(0.503) 		1
(1.00) 		0.023
(0.502) 		0.591
(1.00) 		1
(1.00) 		0.0183
(0.475) 		0.388
(0.929) 		0.106
(0.723) 		0.246
(0.837) 		0.0146
(0.446)
18q loss 46 (42%) 64 0.679
(1.00) 		0.768
(1.00) 		0.431
(0.952) 		0.064
(0.67) 		0.551
(0.994) 		1
(1.00) 		0.893
(1.00) 		0.0656
(0.67) 		1
(1.00) 		0.0266
(0.517) 		0.717
(1.00) 		0.626
(1.00) 		0.0125
(0.421) 		0.979
(1.00) 		0.117
(0.737) 		0.248
(0.837) 		0.0296
(0.543)
19q loss 35 (32%) 75 0.0435
(0.604) 		0.484
(0.969) 		0.242
(0.837) 		0.432
(0.952) 		0.0524
(0.651) 		0.46
(0.956) 		0.78
(1.00) 		0.583
(1.00) 		1
(1.00) 		0.196
(0.814) 		0.18
(0.794) 		0.289
(0.876) 		0.0354
(0.576) 		0.754
(1.00) 		1
(1.00) 		0.867
(1.00) 		0.539
(0.994)
20p loss 26 (24%) 84 0.648
(1.00) 		0.89
(1.00) 		0.282
(0.876) 		0.906
(1.00) 		0.34
(0.901) 		0.159
(0.78) 		0.27
(0.866) 		0.0234
(0.503) 		1
(1.00) 		0.0577
(0.651) 		1
(1.00) 		1
(1.00) 		0.518
(0.985) 		0.967
(1.00) 		0.647
(1.00) 		0.854
(1.00) 		1
(1.00)
20q loss 21 (19%) 89 0.925
(1.00) 		0.769
(1.00) 		0.276
(0.873) 		0.525
(0.985) 		0.453
(0.956) 		0.508
(0.983) 		0.702
(1.00) 		0.0596
(0.651) 		0.53
(0.99) 		0.198
(0.818) 		1
(1.00) 		0.342
(0.901) 		0.682
(1.00) 		0.705
(1.00) 		0.633
(1.00) 		0.905
(1.00) 		1
(1.00)
xp loss 13 (12%) 97 0.934
(1.00) 		0.0853
(0.688) 		0.624
(1.00) 		0.954
(1.00) 		0.248
(0.837) 		0.492
(0.971) 		0.376
(0.926) 		0.996
(1.00) 		1
(1.00) 		0.00927
(0.365) 		1
(1.00) 		1
(1.00) 		0.818
(1.00) 		0.0504
(0.651) 		0.231
(0.833) 		0.35
(0.912) 		0.38
(0.926)
xq loss 11 (10%) 99 0.341
(0.901) 		0.0837
(0.688) 		0.757
(1.00) 		0.667
(1.00) 		0.511
(0.984) 		0.708
(1.00) 		0.646
(1.00) 		0.661
(1.00) 		1
(1.00) 		0.00646
(0.304) 		1
(1.00) 		1
(1.00) 		0.972
(1.00) 		0.0438
(0.604) 		0.2
(0.818) 		0.552
(0.994) 		0.52
(0.985)
'5q gain' versus 'SMOKER'

P value = 0.00113 (Fisher's exact test), Q value = 0.2

Table S1.  Gene #10: '5q gain' versus Clinical Feature #15: 'SMOKER'

nPatients NON-SMOKER SMOKER
ALL 46 61
5Q GAIN MUTATED 18 7
5Q GAIN WILD-TYPE 28 54

Figure S1.  Get High-res Image Gene #10: '5q gain' versus Clinical Feature #15: 'SMOKER'

'14q gain' versus 'YEARS_TO_BIRTH'

P value = 0.00306 (Wilcoxon-test), Q value = 0.24

Table S2.  Gene #28: '14q gain' versus Clinical Feature #8: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 110 62.6 (9.6)
14Q GAIN MUTATED 27 57.9 (8.2)
14Q GAIN WILD-TYPE 83 64.1 (9.6)

Figure S2.  Get High-res Image Gene #28: '14q gain' versus Clinical Feature #8: 'YEARS_TO_BIRTH'

'xp gain' versus 'ORIGIN_ASIA'

P value = 0.00288 (Fisher's exact test), Q value = 0.24

Table S3.  Gene #44: 'xp gain' versus Clinical Feature #17: 'ORIGIN_ASIA'

nPatients ASIAN WESTERN
ALL 63 45
XP GAIN MUTATED 34 11
XP GAIN WILD-TYPE 29 34

Figure S3.  Get High-res Image Gene #44: 'xp gain' versus Clinical Feature #17: 'ORIGIN_ASIA'

'1p loss' versus 'YEARS_TO_BIRTH'

P value = 0.00351 (Wilcoxon-test), Q value = 0.25

Table S4.  Gene #48: '1p loss' versus Clinical Feature #8: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 110 62.6 (9.6)
1P LOSS MUTATED 16 56.6 (7.4)
1P LOSS WILD-TYPE 94 63.6 (9.6)

Figure S4.  Get High-res Image Gene #48: '1p loss' versus Clinical Feature #8: 'YEARS_TO_BIRTH'

'2p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00274 (Wilcoxon-test), Q value = 0.24

Table S5.  Gene #50: '2p loss' versus Clinical Feature #5: 'PATHOLOGY_T_STAGE'

T1 T2 T3
ALL 27 70 13
2P LOSS MUTATED 4 1 3
2P LOSS WILD-TYPE 23 69 10

Figure S5.  Get High-res Image Gene #50: '2p loss' versus Clinical Feature #5: 'PATHOLOGY_T_STAGE'

'4q loss' versus 'BMI'

P value = 0.00176 (Fisher's exact test), Q value = 0.24

Table S6.  Gene #55: '4q loss' versus Clinical Feature #13: 'BMI'

nPatients NORMAL OBESE OVERWEIGHT SEVERELY OBESE UNDERWEIGHT
ALL 53 10 28 3 16
4Q LOSS MUTATED 9 3 0 0 7
4Q LOSS WILD-TYPE 44 7 28 3 9

Figure S6.  Get High-res Image Gene #55: '4q loss' versus Clinical Feature #13: 'BMI'

'6p loss' versus 'YEARS_TO_BIRTH'

P value = 0.00101 (Wilcoxon-test), Q value = 0.2

Table S7.  Gene #58: '6p loss' versus Clinical Feature #8: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 110 62.6 (9.6)
6P LOSS MUTATED 19 55.9 (8.6)
6P LOSS WILD-TYPE 91 64.0 (9.3)

Figure S7.  Get High-res Image Gene #58: '6p loss' versus Clinical Feature #8: 'YEARS_TO_BIRTH'

'6p loss' versus 'ORIGIN_ASIA'

P value = 0.00206 (Fisher's exact test), Q value = 0.24

Table S8.  Gene #58: '6p loss' versus Clinical Feature #17: 'ORIGIN_ASIA'

nPatients ASIAN WESTERN
ALL 63 45
6P LOSS MUTATED 17 2
6P LOSS WILD-TYPE 46 43

Figure S8.  Get High-res Image Gene #58: '6p loss' versus Clinical Feature #17: 'ORIGIN_ASIA'

'13q loss' versus 'ORIGIN_ASIA'

P value = 0.0033 (Fisher's exact test), Q value = 0.24

Table S9.  Gene #73: '13q loss' versus Clinical Feature #17: 'ORIGIN_ASIA'

nPatients ASIAN WESTERN
ALL 63 45
13Q LOSS MUTATED 35 12
13Q LOSS WILD-TYPE 28 33

Figure S9.  Get High-res Image Gene #73: '13q loss' versus Clinical Feature #17: 'ORIGIN_ASIA'

'14p loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00257 (Wilcoxon-test), Q value = 0.24

Table S10.  Gene #74: '14p loss' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 70 81.7 (9.0)
14P LOSS MUTATED 23 86.1 (8.4)
14P LOSS WILD-TYPE 47 79.6 (8.6)

Figure S10.  Get High-res Image Gene #74: '14p loss' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'

'14p loss' versus 'COUNTRY_OF_ORIGIN'

P value = 0.00332 (Fisher's exact test), Q value = 0.24

Table S11.  Gene #74: '14p loss' versus Clinical Feature #16: 'COUNTRY_OF_ORIGIN'

nPatients BULGARIA CANADA CHINA JAMAICA MEXICO POLAND RUSSIA UKRAINE UNITED STATES VIETNAM
ALL 2 1 18 1 2 2 1 3 33 45
14P LOSS MUTATED 2 1 10 0 0 0 1 2 10 8
14P LOSS WILD-TYPE 0 0 8 1 2 2 0 1 23 37

Figure S11.  Get High-res Image Gene #74: '14p loss' versus Clinical Feature #16: 'COUNTRY_OF_ORIGIN'

'14q loss' versus 'COUNTRY_OF_ORIGIN'

P value = 0.00276 (Fisher's exact test), Q value = 0.24

Table S12.  Gene #75: '14q loss' versus Clinical Feature #16: 'COUNTRY_OF_ORIGIN'

nPatients BULGARIA CANADA CHINA JAMAICA MEXICO POLAND RUSSIA UKRAINE UNITED STATES VIETNAM
ALL 2 1 18 1 2 2 1 3 33 45
14Q LOSS MUTATED 2 0 3 0 0 0 1 1 1 2
14Q LOSS WILD-TYPE 0 1 15 1 2 2 0 2 32 43

Figure S12.  Get High-res Image Gene #75: '14q loss' versus Clinical Feature #16: 'COUNTRY_OF_ORIGIN'

'19p loss' versus 'BMI'

P value = 0.00068 (Fisher's exact test), Q value = 0.2

Table S13.  Gene #84: '19p loss' versus Clinical Feature #13: 'BMI'

nPatients NORMAL OBESE OVERWEIGHT SEVERELY OBESE UNDERWEIGHT
ALL 53 10 28 3 16
19P LOSS MUTATED 22 7 4 3 9
19P LOSS WILD-TYPE 31 3 24 0 7

Figure S13.  Get High-res Image Gene #84: '19p loss' versus Clinical Feature #13: 'BMI'

'21p loss' versus 'BMI'

P value = 0.00151 (Fisher's exact test), Q value = 0.22

Table S14.  Gene #88: '21p loss' versus Clinical Feature #13: 'BMI'

nPatients NORMAL OBESE OVERWEIGHT SEVERELY OBESE UNDERWEIGHT
ALL 53 10 28 3 16
21P LOSS MUTATED 28 4 3 2 5
21P LOSS WILD-TYPE 25 6 25 1 11

Figure S14.  Get High-res Image Gene #88: '21p loss' versus Clinical Feature #13: 'BMI'

'21q loss' versus 'BMI'

P value = 0.00138 (Fisher's exact test), Q value = 0.22

Table S15.  Gene #89: '21q loss' versus Clinical Feature #13: 'BMI'

nPatients NORMAL OBESE OVERWEIGHT SEVERELY OBESE UNDERWEIGHT
ALL 53 10 28 3 16
21Q LOSS MUTATED 25 4 2 2 5
21Q LOSS WILD-TYPE 28 6 26 1 11

Figure S15.  Get High-res Image Gene #89: '21q loss' versus Clinical Feature #13: 'BMI'

'22p loss' versus 'BMI'

P value = 0.00305 (Fisher's exact test), Q value = 0.24

Table S16.  Gene #90: '22p loss' versus Clinical Feature #13: 'BMI'

nPatients NORMAL OBESE OVERWEIGHT SEVERELY OBESE UNDERWEIGHT
ALL 53 10 28 3 16
22P LOSS MUTATED 27 4 4 2 10
22P LOSS WILD-TYPE 26 6 24 1 6

Figure S16.  Get High-res Image Gene #90: '22p loss' versus Clinical Feature #13: 'BMI'

'22p loss' versus 'COUNTRY_OF_ORIGIN'

P value = 0.00103 (Fisher's exact test), Q value = 0.2

Table S17.  Gene #90: '22p loss' versus Clinical Feature #16: 'COUNTRY_OF_ORIGIN'

nPatients BULGARIA CANADA CHINA JAMAICA MEXICO POLAND RUSSIA UKRAINE UNITED STATES VIETNAM
ALL 2 1 18 1 2 2 1 3 33 45
22P LOSS MUTATED 2 0 10 0 0 0 1 0 7 26
22P LOSS WILD-TYPE 0 1 8 1 2 2 0 3 26 19

Figure S17.  Get High-res Image Gene #90: '22p loss' versus Clinical Feature #16: 'COUNTRY_OF_ORIGIN'

'22p loss' versus 'ORIGIN_ASIA'

P value = 0.000359 (Fisher's exact test), Q value = 0.19

Table S18.  Gene #90: '22p loss' versus Clinical Feature #17: 'ORIGIN_ASIA'

nPatients ASIAN WESTERN
ALL 63 45
22P LOSS MUTATED 36 10
22P LOSS WILD-TYPE 27 35

Figure S18.  Get High-res Image Gene #90: '22p loss' versus Clinical Feature #17: 'ORIGIN_ASIA'

'22q loss' versus 'BMI'

P value = 0.00217 (Fisher's exact test), Q value = 0.24

Table S19.  Gene #91: '22q loss' versus Clinical Feature #13: 'BMI'

nPatients NORMAL OBESE OVERWEIGHT SEVERELY OBESE UNDERWEIGHT
ALL 53 10 28 3 16
22Q LOSS MUTATED 28 5 4 2 10
22Q LOSS WILD-TYPE 25 5 24 1 6

Figure S19.  Get High-res Image Gene #91: '22q loss' versus Clinical Feature #13: 'BMI'

'22q loss' versus 'COUNTRY_OF_ORIGIN'

P value = 0.00027 (Fisher's exact test), Q value = 0.19

Table S20.  Gene #91: '22q loss' versus Clinical Feature #16: 'COUNTRY_OF_ORIGIN'

nPatients BULGARIA CANADA CHINA JAMAICA MEXICO POLAND RUSSIA UKRAINE UNITED STATES VIETNAM
ALL 2 1 18 1 2 2 1 3 33 45
22Q LOSS MUTATED 2 0 10 0 0 0 1 1 6 28
22Q LOSS WILD-TYPE 0 1 8 1 2 2 0 2 27 17

Figure S20.  Get High-res Image Gene #91: '22q loss' versus Clinical Feature #16: 'COUNTRY_OF_ORIGIN'

'22q loss' versus 'ORIGIN_ASIA'

P value = 8.9e-05 (Fisher's exact test), Q value = 0.14

Table S21.  Gene #91: '22q loss' versus Clinical Feature #17: 'ORIGIN_ASIA'

nPatients ASIAN WESTERN
ALL 63 45
22Q LOSS MUTATED 38 10
22Q LOSS WILD-TYPE 25 35

Figure S21.  Get High-res Image Gene #91: '22q loss' versus Clinical Feature #17: 'ORIGIN_ASIA'

'yp loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00083 (Fisher's exact test), Q value = 0.2

Table S22.  Gene #94: 'yp loss' versus Clinical Feature #7: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IV
ALL 2 22 34 17 13 1 20 1
YP LOSS MUTATED 1 11 29 6 8 0 7 1
YP LOSS WILD-TYPE 1 11 5 11 5 1 13 0

Figure S22.  Get High-res Image Gene #94: 'yp loss' versus Clinical Feature #7: 'PATHOLOGIC_STAGE'

'yq loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00075 (Fisher's exact test), Q value = 0.2

Table S23.  Gene #95: 'yq loss' versus Clinical Feature #7: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IV
ALL 2 22 34 17 13 1 20 1
YQ LOSS MUTATED 1 12 29 6 8 0 7 1
YQ LOSS WILD-TYPE 1 10 5 11 5 1 13 0

Figure S23.  Get High-res Image Gene #95: 'yq loss' versus Clinical Feature #7: 'PATHOLOGIC_STAGE'

Methods & Data
Input

  • Copy number data file = broad_values_by_arm.txt from GISTIC pipeline

  • Processed Copy number data file = /cromwell_root/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a/069a11b4-7b1a-48bc-8231-942ea7a19e7c/correlate_genomic_events_all/abf2ca5c-bd5f-4d49-8b37-7914065d06a1/call-preprocess_genomic_event/transformed.cor.cli.txt

  • Clinical data file = /cromwell_root/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a/39eab10a-1791-41cf-866c-13e6472ce02e/normalize_clinical_cptac/df4eac3a-77b6-4ce7-961f-e1027c1ad609/call-normalize_clinical_cptac_task_1/CPTAC3-LUAD-TP.clin.merged.picked.txt

  • Number of patients = 110

  • Number of significantly arm-level cnvs = 95

  • Number of selected clinical features = 17

  • 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.

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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