Correlation between copy number variation genes (focal events) 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 copy number variation (cnv focal) genes and selected clinical features.

Summary

Testing the association between copy number variation 51 focal events and 17 clinical features across 110 patients, 86 significant findings detected with Q value < 0.25.

  • amp_1q21.2 cnv correlated to 'NUMBER_PACK_YEARS_SMOKED'.

  • amp_4q12 cnv correlated to 'ORIGIN_ASIA'.

  • amp_5p15.33 cnv correlated to 'PATHOLOGY_N_STAGE'.

  • amp_5q35.1 cnv correlated to 'GENDER',  'SMOKER', and 'COUNTRY_OF_ORIGIN'.

  • amp_6q27 cnv correlated to 'COUNTRY_OF_ORIGIN' and 'ORIGIN_ASIA'.

  • amp_7p11.2 cnv correlated to 'HISTOLOGICAL_TYPE',  'COUNTRY_OF_ORIGIN', and 'ORIGIN_ASIA'.

  • amp_8q13.1 cnv correlated to 'COUNTRY_OF_ORIGIN' and 'ORIGIN_ASIA'.

  • amp_8q24.21 cnv correlated to 'BMI',  'COUNTRY_OF_ORIGIN', and 'ORIGIN_ASIA'.

  • amp_8q24.3 cnv correlated to 'COUNTRY_OF_ORIGIN' and 'ORIGIN_ASIA'.

  • amp_11q13.3 cnv correlated to 'BMI'.

  • amp_12p13.33 cnv correlated to 'YEARS_TO_BIRTH' and 'ORIGIN_ASIA'.

  • amp_12p11.21 cnv correlated to 'ORIGIN_ASIA'.

  • amp_12q15 cnv correlated to 'PATHOLOGY_N_STAGE'.

  • amp_14q13.3 cnv correlated to 'YEARS_TO_BIRTH',  'BMI',  'COUNTRY_OF_ORIGIN', and 'ORIGIN_ASIA'.

  • amp_14q32.33 cnv correlated to 'HISTOLOGICAL_TYPE',  'YEARS_TO_BIRTH',  'SMOKER',  'COUNTRY_OF_ORIGIN', and 'ORIGIN_ASIA'.

  • amp_17q23.1 cnv correlated to 'PATHOLOGY_N_STAGE'.

  • amp_20q13.2 cnv correlated to 'DAYS_TO_DEATH_OR_LAST_FUP',  'HISTOLOGIC_GRADE', and 'ORIGIN_ASIA'.

  • amp_20q13.33 cnv correlated to 'DAYS_TO_DEATH_OR_LAST_FUP',  'HISTOLOGIC_GRADE',  'KARNOFSKY_PERFORMANCE_SCORE', and 'YEARS_TO_BIRTH'.

  • amp_xp22.33 cnv correlated to 'PATHOLOGIC_STAGE',  'COUNTRY_OF_ORIGIN', and 'ORIGIN_ASIA'.

  • amp_xq27.3 cnv correlated to 'COUNTRY_OF_ORIGIN' and 'ORIGIN_ASIA'.

  • del_3p24.1 cnv correlated to 'PATHOLOGY_T_STAGE' and 'YEARS_TO_BIRTH'.

  • del_5q15 cnv correlated to 'COUNTRY_OF_ORIGIN' and 'ORIGIN_ASIA'.

  • del_6p11.2 cnv correlated to 'YEARS_TO_BIRTH'.

  • del_6q16.3 cnv correlated to 'YEARS_TO_BIRTH',  'BMI',  'COUNTRY_OF_ORIGIN', and 'ORIGIN_ASIA'.

  • del_8p23.1 cnv correlated to 'HISTOLOGIC_GRADE',  'BMI', and 'ORIGIN_ASIA'.

  • del_9p23 cnv correlated to 'GENDER'.

  • del_9p21.3 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • del_10q25.1 cnv correlated to 'ORIGIN_ASIA'.

  • del_13q11 cnv correlated to 'YEARS_TO_BIRTH',  'BMI',  'COUNTRY_OF_ORIGIN', and 'ORIGIN_ASIA'.

  • del_15q13.1 cnv correlated to 'KARNOFSKY_PERFORMANCE_SCORE',  'SMOKER',  'COUNTRY_OF_ORIGIN', and 'ORIGIN_ASIA'.

  • del_17p13.1 cnv correlated to 'BMI'.

  • del_18q21.31 cnv correlated to 'BMI',  'COUNTRY_OF_ORIGIN', and 'ORIGIN_ASIA'.

  • del_19q13.33 cnv correlated to 'GENDER'.

  • del_21p11.2 cnv correlated to 'GENDER'.

  • del_22p11.2 cnv correlated to 'HISTOLOGICAL_TYPE',  'GENDER',  'RADIATION_THERAPY',  'COUNTRY_OF_ORIGIN', and 'ORIGIN_ASIA'.

  • del_22q13.32 cnv correlated to 'BMI',  'COUNTRY_OF_ORIGIN', and 'ORIGIN_ASIA'.

  • del_xp22.33 cnv correlated to 'GENDER'.

  • del_xq28 cnv correlated to 'KARNOFSKY_PERFORMANCE_SCORE' and 'COUNTRY_OF_ORIGIN'.

  • del_yq11.223 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 51 focal events and 17 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 86 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
amp 14q32 33 46 (42%) 64 0.319
(0.769) 		0.0147
(0.19) 		0.556
(0.911) 		0.857
(1.00) 		0.626
(0.928) 		0.479
(0.89) 		0.74
(0.976) 		0.000392
(0.034) 		1
(1.00) 		0.841
(1.00) 		0.485
(0.893) 		0.0295
(0.266) 		0.334
(0.775) 		0.72
(0.96) 		0.00311
(0.0929) 		0.00132
(0.0636) 		0.000704
(0.0423)
del 22p11 2 44 (40%) 66 0.37
(0.812) 		0.00584
(0.12) 		0.319
(0.769) 		0.325
(0.773) 		0.165
(0.612) 		0.957
(1.00) 		0.632
(0.928) 		0.171
(0.618) 		0.477
(0.89) 		0.0231
(0.236) 		1
(1.00) 		0.0112
(0.164) 		0.133
(0.567) 		0.213
(0.663) 		0.557
(0.911) 		0.00956
(0.149) 		0.00916
(0.149)
amp 14q13 3 62 (56%) 48 0.513
(0.908) 		0.0474
(0.359) 		0.0469
(0.359) 		0.863
(1.00) 		0.206
(0.663) 		0.625
(0.928) 		0.341
(0.781) 		0.0074
(0.134) 		0.538
(0.908) 		1
(1.00) 		0.751
(0.981) 		0.142
(0.58) 		0.00038
(0.034) 		0.869
(1.00) 		0.0501
(0.359) 		0.0007
(0.0423) 		0.000346
(0.034)
amp 20q13 33 51 (46%) 59 0.00636
(0.123) 		0.549
(0.908) 		0.0171
(0.2) 		0.0179
(0.204) 		0.92
(1.00) 		0.813
(0.995) 		0.476
(0.89) 		0.0219
(0.229) 		0.538
(0.908) 		1
(1.00) 		0.783
(0.993) 		0.33
(0.773) 		0.688
(0.956) 		0.511
(0.908) 		0.0833
(0.458) 		0.0805
(0.454) 		0.0495
(0.359)
del 6q16 3 58 (53%) 52 0.859
(1.00) 		0.536
(0.908) 		0.156
(0.607) 		0.0986
(0.488) 		0.365
(0.808) 		0.329
(0.773) 		0.22
(0.678) 		0.00481
(0.107) 		0.278
(0.73) 		1
(1.00) 		1
(1.00) 		0.149
(0.595) 		0.00056
(0.0423) 		0.163
(0.611) 		0.118
(0.544) 		0.00404
(0.1) 		0.000853
(0.0438)
del 13q11 64 (58%) 46 0.0755
(0.437) 		0.139
(0.576) 		0.58
(0.921) 		0.0702
(0.417) 		0.6
(0.927) 		0.0626
(0.393) 		0.212
(0.663) 		0.00856
(0.144) 		0.54
(0.908) 		1
(1.00) 		1
(1.00) 		0.467
(0.884) 		0.00434
(0.102) 		0.775
(0.99) 		0.0477
(0.359) 		0.0001
(0.0173) 		6.72e-05
(0.0152)
del 15q13 1 64 (58%) 46 0.37
(0.812) 		0.603
(0.927) 		0.184
(0.64) 		0.0124
(0.174) 		1
(1.00) 		0.0583
(0.386) 		0.265
(0.724) 		0.21
(0.663) 		1
(1.00) 		0.414
(0.852) 		1
(1.00) 		0.805
(0.995) 		0.131
(0.563) 		0.134
(0.568) 		0.0173
(0.2) 		0.00593
(0.12) 		0.0101
(0.152)
amp 5q35 1 35 (32%) 75 0.0911
(0.473) 		0.575
(0.921) 		0.449
(0.883) 		0.061
(0.392) 		0.514
(0.908) 		0.109
(0.515) 		0.515
(0.908) 		0.164
(0.611) 		0.53
(0.908) 		0.00946
(0.149) 		1
(1.00) 		1
(1.00) 		0.202
(0.663) 		0.308
(0.764) 		0.00576
(0.12) 		0.00775
(0.137) 		0.0364
(0.307)
amp 7p11 2 63 (57%) 47 0.766
(0.989) 		0.0209
(0.224) 		0.0623
(0.393) 		0.636
(0.929) 		0.713
(0.96) 		0.207
(0.663) 		0.39
(0.828) 		0.228
(0.691) 		0.275
(0.73) 		1
(1.00) 		1
(1.00) 		0.138
(0.576) 		0.198
(0.657) 		0.443
(0.878) 		0.556
(0.911) 		0.0019
(0.0762) 		0.000732
(0.0423)
amp 8q24 21 65 (59%) 45 0.865
(1.00) 		0.173
(0.618) 		0.32
(0.769) 		0.77
(0.989) 		0.708
(0.96) 		1
(1.00) 		0.628
(0.928) 		0.269
(0.726) 		1
(1.00) 		0.539
(0.908) 		0.75
(0.98) 		0.467
(0.884) 		0.00189
(0.0762) 		0.105
(0.5) 		0.43
(0.866) 		7e-05
(0.0152) 		1.1e-05
(0.0077)
amp 20q13 2 51 (46%) 59 0.00676
(0.127) 		0.21
(0.663) 		0.00238
(0.0825) 		0.263
(0.721) 		0.918
(1.00) 		0.627
(0.928) 		0.456
(0.884) 		0.0273
(0.26) 		0.538
(0.908) 		1
(1.00) 		0.783
(0.993) 		0.33
(0.773) 		0.419
(0.86) 		0.771
(0.989) 		0.0341
(0.295) 		0.0949
(0.483) 		0.0182
(0.205)
amp xp22 33 46 (42%) 64 0.553
(0.911) 		0.0969
(0.483) 		0.812
(0.995) 		0.843
(1.00) 		0.775
(0.99) 		0.158
(0.607) 		0.0173
(0.2) 		0.487
(0.893) 		1
(1.00) 		0.683
(0.956) 		1
(1.00) 		0.806
(0.995) 		0.242
(0.703) 		0.185
(0.64) 		0.0497
(0.359) 		0.00581
(0.12) 		0.00157
(0.0715)
del 8p23 1 58 (53%) 52 0.372
(0.813) 		0.579
(0.921) 		0.012
(0.173) 		0.638
(0.929) 		1
(1.00) 		0.28
(0.731) 		0.952
(1.00) 		0.252
(0.709) 		0.243
(0.705) 		0.686
(0.956) 		0.839
(1.00) 		1
(1.00) 		0.00249
(0.083) 		0.235
(0.701) 		0.24
(0.703) 		0.084
(0.458) 		0.0189
(0.207)
del 18q21 31 61 (55%) 49 0.583
(0.923) 		0.725
(0.963) 		0.333
(0.775) 		0.0282
(0.26) 		0.576
(0.921) 		0.545
(0.908) 		0.535
(0.908) 		0.0533
(0.37) 		1
(1.00) 		0.223
(0.686) 		0.841
(1.00) 		0.809
(0.995) 		0.00023
(0.0285) 		0.161
(0.607) 		0.44
(0.877) 		0.0144
(0.19) 		0.00351
(0.0965)
del 22q13 32 55 (50%) 55 0.631
(0.928) 		0.66
(0.949) 		0.226
(0.691) 		0.354
(0.794) 		0.611
(0.928) 		0.329
(0.773) 		0.684
(0.956) 		0.381
(0.823) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.0298
(0.266) 		0.00743
(0.134) 		0.482
(0.891) 		0.244
(0.705) 		0.016
(0.2) 		0.0187
(0.207)
amp 6q27 41 (37%) 69 0.142
(0.58) 		0.0281
(0.26) 		0.21
(0.663) 		0.926
(1.00) 		0.125
(0.548) 		0.667
(0.954) 		0.436
(0.871) 		0.211
(0.663) 		1
(1.00) 		0.534
(0.908) 		1
(1.00) 		0.321
(0.769) 		0.65
(0.937) 		0.705
(0.959) 		0.684
(0.956) 		0.00064
(0.0423) 		0.00238
(0.0825)
amp 8q13 1 47 (43%) 63 0.385
(0.824) 		0.32
(0.769) 		0.909
(1.00) 		0.906
(1.00) 		0.389
(0.828) 		0.844
(1.00) 		0.986
(1.00) 		0.267
(0.726) 		1
(1.00) 		0.542
(0.908) 		0.636
(0.929) 		0.146
(0.587) 		0.0258
(0.254) 		0.41
(0.849) 		1
(1.00) 		0.0167
(0.2) 		0.00288
(0.0925)
amp 8q24 3 69 (63%) 41 0.208
(0.663) 		0.342
(0.781) 		0.173
(0.618) 		0.188
(0.642) 		0.644
(0.933) 		0.559
(0.911) 		0.712
(0.96) 		0.086
(0.461) 		1
(1.00) 		0.678
(0.956) 		0.84
(1.00) 		0.316
(0.769) 		0.0671
(0.402) 		0.14
(0.576) 		0.843
(1.00) 		0.00022
(0.0285) 		1.78e-05
(0.0077)
amp 12p13 33 54 (49%) 56 0.0847
(0.459) 		0.49
(0.896) 		0.102
(0.498) 		0.763
(0.988) 		0.471
(0.887) 		0.879
(1.00) 		0.856
(1.00) 		0.00419
(0.101) 		0.537
(0.908) 		0.23
(0.692) 		0.754
(0.982) 		0.229
(0.691) 		0.789
(0.993) 		0.167
(0.615) 		0.0517
(0.368) 		0.028
(0.26) 		0.00344
(0.0965)
amp xq27 3 60 (55%) 50 0.323
(0.769) 		0.197
(0.656) 		0.0642
(0.395) 		0.979
(1.00) 		0.781
(0.993) 		0.569
(0.917) 		0.688
(0.956) 		0.16
(0.607) 		0.241
(0.703) 		0.227
(0.691) 		1
(1.00) 		0.467
(0.884) 		0.121
(0.544) 		0.246
(0.707) 		0.122
(0.544) 		0.00356
(0.0965) 		0.00301
(0.0929)
del 3p24 1 53 (48%) 57 0.955
(1.00) 		0.395
(0.83) 		0.0399
(0.321) 		0.302
(0.754) 		0.0141
(0.188) 		0.847
(1.00) 		0.871
(1.00) 		0.0161
(0.2) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.519
(0.908) 		0.716
(0.96) 		1
(1.00) 		0.481
(0.89) 		0.562
(0.911)
del 5q15 43 (39%) 67 0.252
(0.709) 		0.296
(0.744) 		0.373
(0.813) 		0.064
(0.395) 		0.915
(1.00) 		0.588
(0.923) 		0.18
(0.632) 		0.518
(0.908) 		1
(1.00) 		0.0378
(0.309) 		0.589
(0.923) 		0.613
(0.928) 		0.228
(0.691) 		0.302
(0.754) 		1
(1.00) 		0.00452
(0.103) 		0.0101
(0.152)
del xq28 24 (22%) 86 0.996
(1.00) 		0.344
(0.782) 		0.921
(1.00) 		0.00195
(0.0762) 		0.547
(0.908) 		0.395
(0.83) 		0.719
(0.96) 		0.0873
(0.465) 		0.362
(0.804) 		0.151
(0.596) 		1
(1.00) 		1
(1.00) 		0.0808
(0.454) 		0.107
(0.505) 		0.352
(0.794) 		0.00397
(0.1) 		0.24
(0.703)
amp 1q21 2 89 (81%) 21 0.58
(0.921) 		0.631
(0.928) 		0.421
(0.861) 		0.333
(0.775) 		0.453
(0.884) 		0.873
(1.00) 		0.51
(0.908) 		0.755
(0.983) 		0.172
(0.618) 		1
(1.00) 		1
(1.00) 		0.384
(0.824) 		0.864
(1.00) 		0.00959
(0.149) 		0.633
(0.928) 		0.361
(0.804) 		0.624
(0.928)
amp 4q12 20 (18%) 90 0.469
(0.887) 		0.883
(1.00) 		0.749
(0.98) 		0.26
(0.715) 		0.705
(0.959) 		0.933
(1.00) 		0.692
(0.956) 		0.175
(0.618) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.715
(0.96) 		0.71
(0.96) 		0.604
(0.927) 		0.213
(0.663) 		0.0192
(0.209)
amp 5p15 33 76 (69%) 34 0.769
(0.989) 		0.593
(0.924) 		0.567
(0.916) 		0.62
(0.928) 		0.189
(0.642) 		0.0163
(0.2) 		0.292
(0.737) 		0.547
(0.908) 		0.554
(0.911) 		0.663
(0.95) 		0.783
(0.993) 		1
(1.00) 		0.286
(0.734) 		0.791
(0.993) 		0.536
(0.908) 		0.0658
(0.401) 		0.0584
(0.386)
amp 11q13 3 46 (42%) 64 0.868
(1.00) 		0.58
(0.921) 		0.105
(0.5) 		0.715
(0.96) 		0.628
(0.928) 		0.284
(0.734) 		0.187
(0.642) 		0.0765
(0.437) 		1
(1.00) 		0.683
(0.956) 		1
(1.00) 		0.328
(0.773) 		0.00861
(0.144) 		0.801
(0.995) 		1
(1.00) 		0.0631
(0.394) 		0.0296
(0.266)
amp 12p11 21 37 (34%) 73 0.0599
(0.389) 		0.792
(0.993) 		0.795
(0.993) 		0.104
(0.5) 		0.471
(0.887) 		0.0327
(0.286) 		0.204
(0.663) 		0.0997
(0.488) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.0373
(0.309) 		0.52
(0.908) 		0.769
(0.989) 		0.155
(0.607) 		0.131
(0.563) 		0.013
(0.179)
amp 12q15 33 (30%) 77 0.812
(0.995) 		0.823
(1.00) 		0.161
(0.607) 		0.968
(1.00) 		0.316
(0.769) 		0.0216
(0.228) 		0.12
(0.544) 		0.441
(0.877) 		0.548
(0.908) 		0.509
(0.908) 		1
(1.00) 		0.287
(0.734) 		0.194
(0.653) 		0.721
(0.96) 		0.292
(0.737) 		0.979
(1.00) 		0.201
(0.662)
amp 17q23 1 54 (49%) 56 0.124
(0.545) 		0.561
(0.911) 		0.212
(0.663) 		0.0614
(0.392) 		0.0352
(0.302) 		0.0167
(0.2) 		0.235
(0.701) 		0.601
(0.927) 		0.257
(0.714) 		1
(1.00) 		1
(1.00) 		0.627
(0.928) 		0.851
(1.00) 		0.61
(0.927) 		0.847
(1.00) 		0.0922
(0.475) 		0.248
(0.707)
del 6p11 2 12 (11%) 98 0.134
(0.568) 		0.272
(0.728) 		0.313
(0.769) 		0.852
(1.00) 		0.315
(0.769) 		0.0953
(0.483) 		0.0269
(0.259) 		0.0138
(0.187) 		0.0811
(0.454) 		1
(1.00) 		0.696
(0.956) 		0.84
(1.00) 		0.741
(0.976) 		0.759
(0.983) 		0.307
(0.764) 		0.0714
(0.421)
del 9p23 63 (57%) 47 0.949
(1.00) 		0.805
(0.995) 		0.588
(0.923) 		0.25
(0.709) 		0.881
(1.00) 		0.036
(0.306) 		0.722
(0.96) 		0.0533
(0.37) 		0.568
(0.916) 		0.00202
(0.0762) 		1
(1.00) 		0.463
(0.884) 		0.694
(0.956) 		0.959
(1.00) 		0.169
(0.618) 		0.734
(0.973) 		0.694
(0.956)
del 9p21 3 67 (61%) 43 0.353
(0.794) 		0.0229
(0.236) 		0.387
(0.827) 		0.278
(0.73) 		0.398
(0.831) 		0.218
(0.677) 		0.699
(0.957) 		0.27
(0.726) 		0.544
(0.908) 		0.0378
(0.309) 		1
(1.00) 		0.457
(0.884) 		0.647
(0.935) 		0.461
(0.884) 		0.164
(0.611) 		0.429
(0.866) 		0.694
(0.956)
del 10q25 1 39 (35%) 71 0.597
(0.925) 		0.158
(0.607) 		0.123
(0.545) 		0.52
(0.908) 		0.53
(0.908) 		0.285
(0.734) 		0.239
(0.703) 		0.289
(0.735) 		0.53
(0.908) 		0.139
(0.576) 		0.544
(0.908) 		0.794
(0.993) 		0.253
(0.709) 		0.955
(1.00) 		0.312
(0.769) 		0.122
(0.544) 		0.0242
(0.244)
del 17p13 1 75 (68%) 35 0.336
(0.775) 		0.707
(0.96) 		0.63
(0.928) 		0.0862
(0.461) 		1
(1.00) 		0.0672
(0.402) 		0.745
(0.98) 		0.393
(0.83) 		0.604
(0.927) 		1
(1.00) 		0.458
(0.884) 		0.804
(0.995) 		0.00635
(0.123) 		0.0561
(0.383) 		0.536
(0.908) 		0.0308
(0.272) 		0.091
(0.473)
del 19q13 33 43 (39%) 67 0.173
(0.618) 		0.709
(0.96) 		0.747
(0.98) 		0.423
(0.863) 		0.207
(0.663) 		0.704
(0.959) 		0.527
(0.908) 		0.0542
(0.373) 		1
(1.00) 		0.0125
(0.174) 		0.256
(0.714) 		0.448
(0.882) 		0.0879
(0.465) 		0.811
(0.995) 		0.842
(1.00) 		0.922
(1.00) 		0.55
(0.909)
del 21p11 2 66 (60%) 44 0.0388
(0.315) 		0.634
(0.928) 		0.0662
(0.401) 		0.0589
(0.387) 		0.248
(0.707) 		0.838
(1.00) 		0.41
(0.849) 		0.687
(0.956) 		0.105
(0.5) 		0.00399
(0.1) 		0.457
(0.884) 		0.0523
(0.369) 		0.17
(0.618) 		0.475
(0.89) 		0.691
(0.956) 		0.0482
(0.359) 		0.0487
(0.359)
del xp22 33 23 (21%) 87 0.433
(0.868) 		0.273
(0.728) 		1
(1.00) 		0.46
(0.884) 		0.12
(0.544) 		0.144
(0.583) 		0.0574
(0.386) 		0.525
(0.908) 		1
(1.00) 		0.000859
(0.0438) 		0.54
(0.908) 		0.758
(0.983) 		0.633
(0.928) 		0.285
(0.734) 		0.0601
(0.389) 		0.774
(0.99) 		0.465
(0.884)
del yq11 223 69 (63%) 41 0.62
(0.928) 		0.632
(0.928) 		0.197
(0.656) 		0.121
(0.544) 		0.112
(0.521) 		0.177
(0.624) 		0.00823
(0.143) 		0.692
(0.956) 		1
(1.00) 		0.0966
(0.483) 		0.815
(0.996) 		0.619
(0.928) 		0.5
(0.908) 		0.873
(1.00) 		1
(1.00) 		0.0755
(0.437) 		0.547
(0.908)
amp 1p34 2 26 (24%) 84 0.885
(1.00) 		0.991
(1.00) 		0.337
(0.775) 		0.365
(0.808) 		0.499
(0.908) 		0.309
(0.766) 		0.323
(0.769) 		0.819
(1.00) 		0.562
(0.911) 		0.0577
(0.386) 		1
(1.00) 		1
(1.00) 		0.993
(1.00) 		0.341
(0.781) 		0.821
(1.00) 		0.69
(0.956) 		1
(1.00)
amp 6p21 1 44 (40%) 66 0.278
(0.73) 		0.799
(0.995) 		0.905
(1.00) 		0.573
(0.921) 		0.522
(0.908) 		0.589
(0.923) 		0.807
(0.995) 		0.135
(0.57) 		0.548
(0.908) 		0.683
(0.956) 		1
(1.00) 		0.0839
(0.458) 		0.796
(0.993) 		0.879
(1.00) 		0.171
(0.618) 		0.112
(0.521) 		0.112
(0.521)
amp 13q31 1 30 (27%) 80 0.182
(0.636) 		0.281
(0.733) 		0.211
(0.663) 		0.351
(0.794) 		0.536
(0.908) 		0.947
(1.00) 		0.463
(0.884) 		0.584
(0.923) 		0.477
(0.89) 		0.257
(0.714) 		0.43
(0.866) 		0.415
(0.853) 		0.911
(1.00) 		0.0762
(0.437) 		0.0445
(0.347) 		0.315
(0.769) 		0.194
(0.653)
amp 19q12 33 (30%) 77 0.347
(0.787) 		0.674
(0.956) 		0.128
(0.554) 		0.989
(1.00) 		0.39
(0.828) 		0.522
(0.908) 		0.79
(0.993) 		0.906
(1.00) 		0.562
(0.911) 		0.0816
(0.454) 		1
(1.00) 		0.794
(0.993) 		0.463
(0.884) 		0.813
(0.995) 		0.527
(0.908) 		0.0926
(0.475) 		0.673
(0.956)
amp 20p11 21 27 (25%) 83 0.0423
(0.336) 		0.382
(0.823) 		0.321
(0.769) 		0.24
(0.703) 		0.894
(1.00) 		0.672
(0.956) 		0.87
(1.00) 		0.48
(0.89) 		1
(1.00) 		0.36
(0.804) 		1
(1.00) 		0.786
(0.993) 		0.738
(0.976) 		0.286
(0.734) 		0.654
(0.941) 		0.607
(0.927) 		0.371
(0.813)
amp 21p12 24 (22%) 86 0.893
(1.00) 		0.609
(0.927) 		0.278
(0.73) 		0.527
(0.908) 		0.578
(0.921) 		0.374
(0.813) 		0.159
(0.607) 		0.142
(0.58) 		1
(1.00) 		0.464
(0.884) 		1
(1.00) 		1
(1.00) 		0.269
(0.726) 		0.697
(0.956) 		0.159
(0.607) 		0.785
(0.993) 		0.485
(0.893)
amp yq11 223 25 (23%) 85 0.429
(0.866) 		0.428
(0.866) 		0.26
(0.715) 		0.26
(0.715) 		0.368
(0.811) 		0.0489
(0.359) 		0.047
(0.359) 		0.756
(0.983) 		1
(1.00) 		0.0963
(0.483) 		0.545
(0.908) 		0.375
(0.813) 		0.203
(0.663) 		0.585
(0.923) 		0.159
(0.607) 		0.456
(0.884) 		0.645
(0.933)
del 1p13 3 38 (35%) 72 0.15
(0.595) 		0.892
(1.00) 		0.642
(0.932) 		0.722
(0.96) 		0.607
(0.927) 		0.627
(0.928) 		0.89
(1.00) 		0.68
(0.956) 		1
(1.00) 		0.399
(0.831) 		0.591
(0.923) 		0.122
(0.544) 		0.63
(0.928) 		0.678
(0.956) 		0.0256
(0.254) 		0.526
(0.908) 		0.0995
(0.488)
del 4q35 2 37 (34%) 73 0.608
(0.927) 		0.889
(1.00) 		0.59
(0.923) 		0.0895
(0.47) 		1
(1.00) 		0.955
(1.00) 		0.295
(0.743) 		0.595
(0.924) 		0.537
(0.908) 		0.394
(0.83) 		0.251
(0.709) 		0.795
(0.993) 		0.247
(0.707) 		0.944
(1.00) 		0.151
(0.596) 		0.593
(0.924) 		1
(1.00)
del 12p13 1 44 (40%) 66 0.186
(0.641) 		0.83
(1.00) 		0.663
(0.95) 		0.239
(0.703) 		0.336
(0.775) 		0.127
(0.554) 		0.279
(0.73) 		0.272
(0.728) 		0.0721
(0.422) 		0.413
(0.852) 		1
(1.00) 		0.46
(0.884) 		0.436
(0.871) 		0.409
(0.849) 		0.549
(0.908) 		0.199
(0.657) 		0.694
(0.956)
del 16q24 3 42 (38%) 68 0.544
(0.908) 		0.844
(1.00) 		0.265
(0.724) 		0.187
(0.642) 		0.639
(0.93) 		0.194
(0.653) 		0.231
(0.692) 		0.7
(0.958) 		0.537
(0.908) 		1
(1.00) 		0.717
(0.96) 		1
(1.00) 		0.0428
(0.338) 		0.174
(0.618) 		0.688
(0.956) 		0.442
(0.878) 		0.0268
(0.259)
del 21q11 2 25 (23%) 85 0.771
(0.989) 		0.289
(0.735) 		0.604
(0.927) 		0.396
(0.83) 		0.748
(0.98) 		0.431
(0.866) 		0.446
(0.88) 		0.895
(1.00) 		1
(1.00) 		0.337
(0.775) 		1
(1.00) 		0.382
(0.823) 		0.145
(0.583) 		0.739
(0.976) 		0.487
(0.893) 		0.782
(0.993) 		0.356
(0.797)
'amp_1q21.2' versus 'NUMBER_PACK_YEARS_SMOKED'

P value = 0.00959 (Wilcoxon-test), Q value = 0.15

Table S1.  Gene #2: 'amp_1q21.2' versus Clinical Feature #14: 'NUMBER_PACK_YEARS_SMOKED'

nPatients Mean (Std.Dev)
ALL 54 27.3 (23.6)
AMP PEAK 2(1Q21.2) MUTATED 45 23.8 (21.8)
AMP PEAK 2(1Q21.2) WILD-TYPE 9 44.9 (25.6)

Figure S1.  Get High-res Image Gene #2: 'amp_1q21.2' versus Clinical Feature #14: 'NUMBER_PACK_YEARS_SMOKED'

'amp_4q12' versus 'ORIGIN_ASIA'

P value = 0.0192 (Fisher's exact test), Q value = 0.21

Table S2.  Gene #3: 'amp_4q12' versus Clinical Feature #17: 'ORIGIN_ASIA'

nPatients ASIAN WESTERN
ALL 63 45
AMP PEAK 3(4Q12) MUTATED 16 3
AMP PEAK 3(4Q12) WILD-TYPE 47 42

Figure S2.  Get High-res Image Gene #3: 'amp_4q12' versus Clinical Feature #17: 'ORIGIN_ASIA'

'amp_5p15.33' versus 'PATHOLOGY_N_STAGE'

P value = 0.0163 (Wilcoxon-test), Q value = 0.2

Table S3.  Gene #4: 'amp_5p15.33' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

N0 N1 N2
ALL 73 17 19
AMP PEAK 4(5P15.33) MUTATED 49 16 10
AMP PEAK 4(5P15.33) WILD-TYPE 24 1 9

Figure S3.  Get High-res Image Gene #4: 'amp_5p15.33' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'amp_5q35.1' versus 'GENDER'

P value = 0.00946 (Fisher's exact test), Q value = 0.15

Table S4.  Gene #5: 'amp_5q35.1' versus Clinical Feature #10: 'GENDER'

nPatients FEMALE MALE
ALL 37 73
AMP PEAK 5(5Q35.1) MUTATED 18 17
AMP PEAK 5(5Q35.1) WILD-TYPE 19 56

Figure S4.  Get High-res Image Gene #5: 'amp_5q35.1' versus Clinical Feature #10: 'GENDER'

'amp_5q35.1' versus 'SMOKER'

P value = 0.00576 (Fisher's exact test), Q value = 0.12

Table S5.  Gene #5: 'amp_5q35.1' versus Clinical Feature #15: 'SMOKER'

nPatients NON-SMOKER SMOKER
ALL 46 61
AMP PEAK 5(5Q35.1) MUTATED 21 12
AMP PEAK 5(5Q35.1) WILD-TYPE 25 49

Figure S5.  Get High-res Image Gene #5: 'amp_5q35.1' versus Clinical Feature #15: 'SMOKER'

'amp_5q35.1' versus 'COUNTRY_OF_ORIGIN'

P value = 0.00775 (Fisher's exact test), Q value = 0.14

Table S6.  Gene #5: 'amp_5q35.1' 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
AMP PEAK 5(5Q35.1) MUTATED 1 0 13 0 0 0 0 1 7 12
AMP PEAK 5(5Q35.1) WILD-TYPE 1 1 5 1 2 2 1 2 26 33

Figure S6.  Get High-res Image Gene #5: 'amp_5q35.1' versus Clinical Feature #16: 'COUNTRY_OF_ORIGIN'

'amp_6q27' versus 'COUNTRY_OF_ORIGIN'

P value = 0.00064 (Fisher's exact test), Q value = 0.042

Table S7.  Gene #7: 'amp_6q27' 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
AMP PEAK 7(6Q27) MUTATED 0 1 14 0 0 1 0 1 6 17
AMP PEAK 7(6Q27) WILD-TYPE 2 0 4 1 2 1 1 2 27 28

Figure S7.  Get High-res Image Gene #7: 'amp_6q27' versus Clinical Feature #16: 'COUNTRY_OF_ORIGIN'

'amp_6q27' versus 'ORIGIN_ASIA'

P value = 0.00238 (Fisher's exact test), Q value = 0.083

Table S8.  Gene #7: 'amp_6q27' versus Clinical Feature #17: 'ORIGIN_ASIA'

nPatients ASIAN WESTERN
ALL 63 45
AMP PEAK 7(6Q27) MUTATED 31 9
AMP PEAK 7(6Q27) WILD-TYPE 32 36

Figure S8.  Get High-res Image Gene #7: 'amp_6q27' versus Clinical Feature #17: 'ORIGIN_ASIA'

'amp_7p11.2' versus 'HISTOLOGICAL_TYPE'

P value = 0.0209 (Fisher's exact test), Q value = 0.22

Table S9.  Gene #8: 'amp_7p11.2' versus Clinical Feature #2: 'HISTOLOGICAL_TYPE'

nPatients ACINAR ADENOCARCINOMA ADENOCARCINOMA BASALOID SQUAMOUS CELL CARCINOMA INVASIVE MUCINOUS ADENOCARCINOMA LEPIDIC ADENOCARCINOMA MICROPAPILLARY ADENOCARCINOMA OTHER PAPILLARY ADENOCARCINOMA SOLID ADENOCARCINOMA SQUAMOUS CELL CARCINOMA
ALL 13 68 1 3 1 2 7 5 8 2
AMP PEAK 8(7P11.2) MUTATED 6 46 0 0 0 0 4 1 4 2
AMP PEAK 8(7P11.2) WILD-TYPE 7 22 1 3 1 2 3 4 4 0

Figure S9.  Get High-res Image Gene #8: 'amp_7p11.2' versus Clinical Feature #2: 'HISTOLOGICAL_TYPE'

'amp_7p11.2' versus 'COUNTRY_OF_ORIGIN'

P value = 0.0019 (Fisher's exact test), Q value = 0.076

Table S10.  Gene #8: 'amp_7p11.2' 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
AMP PEAK 8(7P11.2) MUTATED 1 1 16 0 0 1 0 1 13 29
AMP PEAK 8(7P11.2) WILD-TYPE 1 0 2 1 2 1 1 2 20 16

Figure S10.  Get High-res Image Gene #8: 'amp_7p11.2' versus Clinical Feature #16: 'COUNTRY_OF_ORIGIN'

'amp_7p11.2' versus 'ORIGIN_ASIA'

P value = 0.000732 (Fisher's exact test), Q value = 0.042

Table S11.  Gene #8: 'amp_7p11.2' versus Clinical Feature #17: 'ORIGIN_ASIA'

nPatients ASIAN WESTERN
ALL 63 45
AMP PEAK 8(7P11.2) MUTATED 45 17
AMP PEAK 8(7P11.2) WILD-TYPE 18 28

Figure S11.  Get High-res Image Gene #8: 'amp_7p11.2' versus Clinical Feature #17: 'ORIGIN_ASIA'

'amp_8q13.1' versus 'COUNTRY_OF_ORIGIN'

P value = 0.0167 (Fisher's exact test), Q value = 0.2

Table S12.  Gene #9: 'amp_8q13.1' 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
AMP PEAK 9(8Q13.1) MUTATED 2 0 9 0 1 0 0 0 8 25
AMP PEAK 9(8Q13.1) WILD-TYPE 0 1 9 1 1 2 1 3 25 20

Figure S12.  Get High-res Image Gene #9: 'amp_8q13.1' versus Clinical Feature #16: 'COUNTRY_OF_ORIGIN'

'amp_8q13.1' versus 'ORIGIN_ASIA'

P value = 0.00288 (Fisher's exact test), Q value = 0.092

Table S13.  Gene #9: 'amp_8q13.1' versus Clinical Feature #17: 'ORIGIN_ASIA'

nPatients ASIAN WESTERN
ALL 63 45
AMP PEAK 9(8Q13.1) MUTATED 34 11
AMP PEAK 9(8Q13.1) WILD-TYPE 29 34

Figure S13.  Get High-res Image Gene #9: 'amp_8q13.1' versus Clinical Feature #17: 'ORIGIN_ASIA'

'amp_8q24.21' versus 'BMI'

P value = 0.00189 (Fisher's exact test), Q value = 0.076

Table S14.  Gene #10: 'amp_8q24.21' versus Clinical Feature #13: 'BMI'

nPatients NORMAL OBESE OVERWEIGHT SEVERELY OBESE UNDERWEIGHT
ALL 53 10 28 3 16
AMP PEAK 10(8Q24.21) MUTATED 40 3 10 2 10
AMP PEAK 10(8Q24.21) WILD-TYPE 13 7 18 1 6

Figure S14.  Get High-res Image Gene #10: 'amp_8q24.21' versus Clinical Feature #13: 'BMI'

'amp_8q24.21' versus 'COUNTRY_OF_ORIGIN'

P value = 7e-05 (Fisher's exact test), Q value = 0.015

Table S15.  Gene #10: 'amp_8q24.21' 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
AMP PEAK 10(8Q24.21) MUTATED 2 0 14 0 1 1 0 0 11 34
AMP PEAK 10(8Q24.21) WILD-TYPE 0 1 4 1 1 1 1 3 22 11

Figure S15.  Get High-res Image Gene #10: 'amp_8q24.21' versus Clinical Feature #16: 'COUNTRY_OF_ORIGIN'

'amp_8q24.21' versus 'ORIGIN_ASIA'

P value = 1.1e-05 (Fisher's exact test), Q value = 0.0077

Table S16.  Gene #10: 'amp_8q24.21' versus Clinical Feature #17: 'ORIGIN_ASIA'

nPatients ASIAN WESTERN
ALL 63 45
AMP PEAK 10(8Q24.21) MUTATED 48 15
AMP PEAK 10(8Q24.21) WILD-TYPE 15 30

Figure S16.  Get High-res Image Gene #10: 'amp_8q24.21' versus Clinical Feature #17: 'ORIGIN_ASIA'

'amp_8q24.3' versus 'COUNTRY_OF_ORIGIN'

P value = 0.00022 (Fisher's exact test), Q value = 0.028

Table S17.  Gene #11: 'amp_8q24.3' 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
AMP PEAK 11(8Q24.3) MUTATED 1 1 14 0 1 1 0 0 13 36
AMP PEAK 11(8Q24.3) WILD-TYPE 1 0 4 1 1 1 1 3 20 9

Figure S17.  Get High-res Image Gene #11: 'amp_8q24.3' versus Clinical Feature #16: 'COUNTRY_OF_ORIGIN'

'amp_8q24.3' versus 'ORIGIN_ASIA'

P value = 1.78e-05 (Fisher's exact test), Q value = 0.0077

Table S18.  Gene #11: 'amp_8q24.3' versus Clinical Feature #17: 'ORIGIN_ASIA'

nPatients ASIAN WESTERN
ALL 63 45
AMP PEAK 11(8Q24.3) MUTATED 50 17
AMP PEAK 11(8Q24.3) WILD-TYPE 13 28

Figure S18.  Get High-res Image Gene #11: 'amp_8q24.3' versus Clinical Feature #17: 'ORIGIN_ASIA'

'amp_11q13.3' versus 'BMI'

P value = 0.00861 (Fisher's exact test), Q value = 0.14

Table S19.  Gene #12: 'amp_11q13.3' versus Clinical Feature #13: 'BMI'

nPatients NORMAL OBESE OVERWEIGHT SEVERELY OBESE UNDERWEIGHT
ALL 53 10 28 3 16
AMP PEAK 12(11Q13.3) MUTATED 28 4 5 0 9
AMP PEAK 12(11Q13.3) WILD-TYPE 25 6 23 3 7

Figure S19.  Get High-res Image Gene #12: 'amp_11q13.3' versus Clinical Feature #13: 'BMI'

'amp_12p13.33' versus 'YEARS_TO_BIRTH'

P value = 0.00419 (Wilcoxon-test), Q value = 0.1

Table S20.  Gene #13: 'amp_12p13.33' versus Clinical Feature #8: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 110 62.6 (9.6)
AMP PEAK 13(12P13.33) MUTATED 54 60.3 (8.6)
AMP PEAK 13(12P13.33) WILD-TYPE 56 64.9 (10.1)

Figure S20.  Get High-res Image Gene #13: 'amp_12p13.33' versus Clinical Feature #8: 'YEARS_TO_BIRTH'

'amp_12p13.33' versus 'ORIGIN_ASIA'

P value = 0.00344 (Fisher's exact test), Q value = 0.096

Table S21.  Gene #13: 'amp_12p13.33' versus Clinical Feature #17: 'ORIGIN_ASIA'

nPatients ASIAN WESTERN
ALL 63 45
AMP PEAK 13(12P13.33) MUTATED 38 14
AMP PEAK 13(12P13.33) WILD-TYPE 25 31

Figure S21.  Get High-res Image Gene #13: 'amp_12p13.33' versus Clinical Feature #17: 'ORIGIN_ASIA'

'amp_12p11.21' versus 'ORIGIN_ASIA'

P value = 0.013 (Fisher's exact test), Q value = 0.18

Table S22.  Gene #14: 'amp_12p11.21' versus Clinical Feature #17: 'ORIGIN_ASIA'

nPatients ASIAN WESTERN
ALL 63 45
AMP PEAK 14(12P11.21) MUTATED 28 9
AMP PEAK 14(12P11.21) WILD-TYPE 35 36

Figure S22.  Get High-res Image Gene #14: 'amp_12p11.21' versus Clinical Feature #17: 'ORIGIN_ASIA'

'amp_12q15' versus 'PATHOLOGY_N_STAGE'

P value = 0.0216 (Wilcoxon-test), Q value = 0.23

Table S23.  Gene #15: 'amp_12q15' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

N0 N1 N2
ALL 73 17 19
AMP PEAK 15(12Q15) MUTATED 16 9 8
AMP PEAK 15(12Q15) WILD-TYPE 57 8 11

Figure S23.  Get High-res Image Gene #15: 'amp_12q15' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'amp_14q13.3' versus 'YEARS_TO_BIRTH'

P value = 0.0074 (Wilcoxon-test), Q value = 0.13

Table S24.  Gene #17: 'amp_14q13.3' versus Clinical Feature #8: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 110 62.6 (9.6)
AMP PEAK 17(14Q13.3) MUTATED 62 60.5 (8.8)
AMP PEAK 17(14Q13.3) WILD-TYPE 48 65.3 (10.1)

Figure S24.  Get High-res Image Gene #17: 'amp_14q13.3' versus Clinical Feature #8: 'YEARS_TO_BIRTH'

'amp_14q13.3' versus 'BMI'

P value = 0.00038 (Fisher's exact test), Q value = 0.034

Table S25.  Gene #17: 'amp_14q13.3' versus Clinical Feature #13: 'BMI'

nPatients NORMAL OBESE OVERWEIGHT SEVERELY OBESE UNDERWEIGHT
ALL 53 10 28 3 16
AMP PEAK 17(14Q13.3) MUTATED 40 6 9 0 7
AMP PEAK 17(14Q13.3) WILD-TYPE 13 4 19 3 9

Figure S25.  Get High-res Image Gene #17: 'amp_14q13.3' versus Clinical Feature #13: 'BMI'

'amp_14q13.3' versus 'COUNTRY_OF_ORIGIN'

P value = 7e-04 (Fisher's exact test), Q value = 0.042

Table S26.  Gene #17: 'amp_14q13.3' 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
AMP PEAK 17(14Q13.3) MUTATED 2 0 14 1 0 0 0 2 11 31
AMP PEAK 17(14Q13.3) WILD-TYPE 0 1 4 0 2 2 1 1 22 14

Figure S26.  Get High-res Image Gene #17: 'amp_14q13.3' versus Clinical Feature #16: 'COUNTRY_OF_ORIGIN'

'amp_14q13.3' versus 'ORIGIN_ASIA'

P value = 0.000346 (Fisher's exact test), Q value = 0.034

Table S27.  Gene #17: 'amp_14q13.3' versus Clinical Feature #17: 'ORIGIN_ASIA'

nPatients ASIAN WESTERN
ALL 63 45
AMP PEAK 17(14Q13.3) MUTATED 45 16
AMP PEAK 17(14Q13.3) WILD-TYPE 18 29

Figure S27.  Get High-res Image Gene #17: 'amp_14q13.3' versus Clinical Feature #17: 'ORIGIN_ASIA'

'amp_14q32.33' versus 'HISTOLOGICAL_TYPE'

P value = 0.0147 (Fisher's exact test), Q value = 0.19

Table S28.  Gene #18: 'amp_14q32.33' versus Clinical Feature #2: 'HISTOLOGICAL_TYPE'

nPatients ACINAR ADENOCARCINOMA ADENOCARCINOMA BASALOID SQUAMOUS CELL CARCINOMA INVASIVE MUCINOUS ADENOCARCINOMA LEPIDIC ADENOCARCINOMA MICROPAPILLARY ADENOCARCINOMA OTHER PAPILLARY ADENOCARCINOMA SOLID ADENOCARCINOMA SQUAMOUS CELL CARCINOMA
ALL 13 68 1 3 1 2 7 5 8 2
AMP PEAK 18(14Q32.33) MUTATED 1 33 0 1 0 2 1 3 5 0
AMP PEAK 18(14Q32.33) WILD-TYPE 12 35 1 2 1 0 6 2 3 2

Figure S28.  Get High-res Image Gene #18: 'amp_14q32.33' versus Clinical Feature #2: 'HISTOLOGICAL_TYPE'

'amp_14q32.33' versus 'YEARS_TO_BIRTH'

P value = 0.000392 (Wilcoxon-test), Q value = 0.034

Table S29.  Gene #18: 'amp_14q32.33' versus Clinical Feature #8: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 110 62.6 (9.6)
AMP PEAK 18(14Q32.33) MUTATED 46 59.1 (8.7)
AMP PEAK 18(14Q32.33) WILD-TYPE 64 65.2 (9.5)

Figure S29.  Get High-res Image Gene #18: 'amp_14q32.33' versus Clinical Feature #8: 'YEARS_TO_BIRTH'

'amp_14q32.33' versus 'SMOKER'

P value = 0.00311 (Fisher's exact test), Q value = 0.093

Table S30.  Gene #18: 'amp_14q32.33' versus Clinical Feature #15: 'SMOKER'

nPatients NON-SMOKER SMOKER
ALL 46 61
AMP PEAK 18(14Q32.33) MUTATED 27 18
AMP PEAK 18(14Q32.33) WILD-TYPE 19 43

Figure S30.  Get High-res Image Gene #18: 'amp_14q32.33' versus Clinical Feature #15: 'SMOKER'

'amp_14q32.33' versus 'COUNTRY_OF_ORIGIN'

P value = 0.00132 (Fisher's exact test), Q value = 0.064

Table S31.  Gene #18: 'amp_14q32.33' 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
AMP PEAK 18(14Q32.33) MUTATED 1 0 10 1 0 1 0 2 5 25
AMP PEAK 18(14Q32.33) WILD-TYPE 1 1 8 0 2 1 1 1 28 20

Figure S31.  Get High-res Image Gene #18: 'amp_14q32.33' versus Clinical Feature #16: 'COUNTRY_OF_ORIGIN'

'amp_14q32.33' versus 'ORIGIN_ASIA'

P value = 0.000704 (Fisher's exact test), Q value = 0.042

Table S32.  Gene #18: 'amp_14q32.33' versus Clinical Feature #17: 'ORIGIN_ASIA'

nPatients ASIAN WESTERN
ALL 63 45
AMP PEAK 18(14Q32.33) MUTATED 35 10
AMP PEAK 18(14Q32.33) WILD-TYPE 28 35

Figure S32.  Get High-res Image Gene #18: 'amp_14q32.33' versus Clinical Feature #17: 'ORIGIN_ASIA'

'amp_17q23.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.0167 (Wilcoxon-test), Q value = 0.2

Table S33.  Gene #19: 'amp_17q23.1' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

N0 N1 N2
ALL 73 17 19
AMP PEAK 19(17Q23.1) MUTATED 39 11 4
AMP PEAK 19(17Q23.1) WILD-TYPE 34 6 15

Figure S33.  Get High-res Image Gene #19: 'amp_17q23.1' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'amp_20q13.2' versus 'DAYS_TO_DEATH_OR_LAST_FUP'

P value = 0.00676 (logrank test), Q value = 0.13

Table S34.  Gene #22: 'amp_20q13.2' versus Clinical Feature #1: 'DAYS_TO_DEATH_OR_LAST_FUP'

nPatients nDeath Duration Range (Median), Month
ALL 110 11 0.2 - 35.0 (13.1)
AMP PEAK 22(20Q13.2) MUTATED 47 1 0.2 - 35.0 (13.6)
AMP PEAK 22(20Q13.2) WILD-TYPE 55 10 0.2 - 27.4 (12.0)

Figure S34.  Get High-res Image Gene #22: 'amp_20q13.2' versus Clinical Feature #1: 'DAYS_TO_DEATH_OR_LAST_FUP'

'amp_20q13.2' versus 'HISTOLOGIC_GRADE'

P value = 0.00238 (Fisher's exact test), Q value = 0.083

Table S35.  Gene #22: 'amp_20q13.2' versus Clinical Feature #3: 'HISTOLOGIC_GRADE'

nPatients G1 G2 G3 G4 GX
ALL 7 65 31 1 6
AMP PEAK 22(20Q13.2) MUTATED 0 35 15 1 0
AMP PEAK 22(20Q13.2) WILD-TYPE 7 30 16 0 6

Figure S35.  Get High-res Image Gene #22: 'amp_20q13.2' versus Clinical Feature #3: 'HISTOLOGIC_GRADE'

'amp_20q13.2' versus 'ORIGIN_ASIA'

P value = 0.0182 (Fisher's exact test), Q value = 0.21

Table S36.  Gene #22: 'amp_20q13.2' versus Clinical Feature #17: 'ORIGIN_ASIA'

nPatients ASIAN WESTERN
ALL 63 45
AMP PEAK 22(20Q13.2) MUTATED 35 14
AMP PEAK 22(20Q13.2) WILD-TYPE 28 31

Figure S36.  Get High-res Image Gene #22: 'amp_20q13.2' versus Clinical Feature #17: 'ORIGIN_ASIA'

'amp_20q13.33' versus 'DAYS_TO_DEATH_OR_LAST_FUP'

P value = 0.00636 (logrank test), Q value = 0.12

Table S37.  Gene #23: 'amp_20q13.33' versus Clinical Feature #1: 'DAYS_TO_DEATH_OR_LAST_FUP'

nPatients nDeath Duration Range (Median), Month
ALL 110 11 0.2 - 35.0 (13.1)
AMP PEAK 23(20Q13.33) MUTATED 48 1 0.2 - 35.0 (13.6)
AMP PEAK 23(20Q13.33) WILD-TYPE 54 10 0.2 - 27.4 (12.0)

Figure S37.  Get High-res Image Gene #23: 'amp_20q13.33' versus Clinical Feature #1: 'DAYS_TO_DEATH_OR_LAST_FUP'

'amp_20q13.33' versus 'HISTOLOGIC_GRADE'

P value = 0.0171 (Fisher's exact test), Q value = 0.2

Table S38.  Gene #23: 'amp_20q13.33' versus Clinical Feature #3: 'HISTOLOGIC_GRADE'

nPatients G1 G2 G3 G4 GX
ALL 7 65 31 1 6
AMP PEAK 23(20Q13.33) MUTATED 1 35 14 1 0
AMP PEAK 23(20Q13.33) WILD-TYPE 6 30 17 0 6

Figure S38.  Get High-res Image Gene #23: 'amp_20q13.33' versus Clinical Feature #3: 'HISTOLOGIC_GRADE'

'amp_20q13.33' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0179 (Wilcoxon-test), Q value = 0.2

Table S39.  Gene #23: 'amp_20q13.33' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 70 81.7 (9.0)
AMP PEAK 23(20Q13.33) MUTATED 35 79.1 (8.2)
AMP PEAK 23(20Q13.33) WILD-TYPE 35 84.3 (9.2)

Figure S39.  Get High-res Image Gene #23: 'amp_20q13.33' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'

'amp_20q13.33' versus 'YEARS_TO_BIRTH'

P value = 0.0219 (Wilcoxon-test), Q value = 0.23

Table S40.  Gene #23: 'amp_20q13.33' versus Clinical Feature #8: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 110 62.6 (9.6)
AMP PEAK 23(20Q13.33) MUTATED 51 60.5 (9.3)
AMP PEAK 23(20Q13.33) WILD-TYPE 59 64.4 (9.7)

Figure S40.  Get High-res Image Gene #23: 'amp_20q13.33' versus Clinical Feature #8: 'YEARS_TO_BIRTH'

'amp_xp22.33' versus 'PATHOLOGIC_STAGE'

P value = 0.0173 (Fisher's exact test), Q value = 0.2

Table S41.  Gene #25: 'amp_xp22.33' 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
AMP PEAK 25(XP22.33) MUTATED 0 10 8 11 4 0 12 1
AMP PEAK 25(XP22.33) WILD-TYPE 2 12 26 6 9 1 8 0

Figure S41.  Get High-res Image Gene #25: 'amp_xp22.33' versus Clinical Feature #7: 'PATHOLOGIC_STAGE'

'amp_xp22.33' versus 'COUNTRY_OF_ORIGIN'

P value = 0.00581 (Fisher's exact test), Q value = 0.12

Table S42.  Gene #25: 'amp_xp22.33' 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
AMP PEAK 25(XP22.33) MUTATED 0 0 14 0 0 1 0 0 10 21
AMP PEAK 25(XP22.33) WILD-TYPE 2 1 4 1 2 1 1 3 23 24

Figure S42.  Get High-res Image Gene #25: 'amp_xp22.33' versus Clinical Feature #16: 'COUNTRY_OF_ORIGIN'

'amp_xp22.33' versus 'ORIGIN_ASIA'

P value = 0.00157 (Fisher's exact test), Q value = 0.072

Table S43.  Gene #25: 'amp_xp22.33' versus Clinical Feature #17: 'ORIGIN_ASIA'

nPatients ASIAN WESTERN
ALL 63 45
AMP PEAK 25(XP22.33) MUTATED 35 11
AMP PEAK 25(XP22.33) WILD-TYPE 28 34

Figure S43.  Get High-res Image Gene #25: 'amp_xp22.33' versus Clinical Feature #17: 'ORIGIN_ASIA'

'amp_xq27.3' versus 'COUNTRY_OF_ORIGIN'

P value = 0.00356 (Fisher's exact test), Q value = 0.096

Table S44.  Gene #26: 'amp_xq27.3' 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
AMP PEAK 26(XQ27.3) MUTATED 2 1 13 0 1 1 1 0 11 30
AMP PEAK 26(XQ27.3) WILD-TYPE 0 0 5 1 1 1 0 3 22 15

Figure S44.  Get High-res Image Gene #26: 'amp_xq27.3' versus Clinical Feature #16: 'COUNTRY_OF_ORIGIN'

'amp_xq27.3' versus 'ORIGIN_ASIA'

P value = 0.00301 (Fisher's exact test), Q value = 0.093

Table S45.  Gene #26: 'amp_xq27.3' versus Clinical Feature #17: 'ORIGIN_ASIA'

nPatients ASIAN WESTERN
ALL 63 45
AMP PEAK 26(XQ27.3) MUTATED 43 17
AMP PEAK 26(XQ27.3) WILD-TYPE 20 28

Figure S45.  Get High-res Image Gene #26: 'amp_xq27.3' versus Clinical Feature #17: 'ORIGIN_ASIA'

'del_3p24.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.0141 (Wilcoxon-test), Q value = 0.19

Table S46.  Gene #29: 'del_3p24.1' versus Clinical Feature #5: 'PATHOLOGY_T_STAGE'

T1 T2 T3
ALL 27 70 13
DEL PEAK 2(3P24.1) MUTATED 13 29 11
DEL PEAK 2(3P24.1) WILD-TYPE 14 41 2

Figure S46.  Get High-res Image Gene #29: 'del_3p24.1' versus Clinical Feature #5: 'PATHOLOGY_T_STAGE'

'del_3p24.1' versus 'YEARS_TO_BIRTH'

P value = 0.0161 (Wilcoxon-test), Q value = 0.2

Table S47.  Gene #29: 'del_3p24.1' versus Clinical Feature #8: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 110 62.6 (9.6)
DEL PEAK 2(3P24.1) MUTATED 53 60.1 (9.6)
DEL PEAK 2(3P24.1) WILD-TYPE 57 64.9 (9.1)

Figure S47.  Get High-res Image Gene #29: 'del_3p24.1' versus Clinical Feature #8: 'YEARS_TO_BIRTH'

'del_5q15' versus 'COUNTRY_OF_ORIGIN'

P value = 0.00452 (Fisher's exact test), Q value = 0.1

Table S48.  Gene #31: 'del_5q15' 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
DEL PEAK 4(5Q15) MUTATED 1 1 6 1 0 0 0 2 6 25
DEL PEAK 4(5Q15) WILD-TYPE 1 0 12 0 2 2 1 1 27 20

Figure S48.  Get High-res Image Gene #31: 'del_5q15' versus Clinical Feature #16: 'COUNTRY_OF_ORIGIN'

'del_5q15' versus 'ORIGIN_ASIA'

P value = 0.0101 (Fisher's exact test), Q value = 0.15

Table S49.  Gene #31: 'del_5q15' versus Clinical Feature #17: 'ORIGIN_ASIA'

nPatients ASIAN WESTERN
ALL 63 45
DEL PEAK 4(5Q15) MUTATED 31 11
DEL PEAK 4(5Q15) WILD-TYPE 32 34

Figure S49.  Get High-res Image Gene #31: 'del_5q15' versus Clinical Feature #17: 'ORIGIN_ASIA'

'del_6p11.2' versus 'YEARS_TO_BIRTH'

P value = 0.0138 (Wilcoxon-test), Q value = 0.19

Table S50.  Gene #32: 'del_6p11.2' versus Clinical Feature #8: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 110 62.6 (9.6)
DEL PEAK 5(6P11.2) MUTATED 12 56.0 (10.4)
DEL PEAK 5(6P11.2) WILD-TYPE 98 63.4 (9.3)

Figure S50.  Get High-res Image Gene #32: 'del_6p11.2' versus Clinical Feature #8: 'YEARS_TO_BIRTH'

'del_6q16.3' versus 'YEARS_TO_BIRTH'

P value = 0.00481 (Wilcoxon-test), Q value = 0.11

Table S51.  Gene #33: 'del_6q16.3' versus Clinical Feature #8: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 110 62.6 (9.6)
DEL PEAK 6(6Q16.3) MUTATED 58 60.1 (9.4)
DEL PEAK 6(6Q16.3) WILD-TYPE 52 65.4 (9.2)

Figure S51.  Get High-res Image Gene #33: 'del_6q16.3' versus Clinical Feature #8: 'YEARS_TO_BIRTH'

'del_6q16.3' versus 'BMI'

P value = 0.00056 (Fisher's exact test), Q value = 0.042

Table S52.  Gene #33: 'del_6q16.3' versus Clinical Feature #13: 'BMI'

nPatients NORMAL OBESE OVERWEIGHT SEVERELY OBESE UNDERWEIGHT
ALL 53 10 28 3 16
DEL PEAK 6(6Q16.3) MUTATED 33 3 7 2 13
DEL PEAK 6(6Q16.3) WILD-TYPE 20 7 21 1 3

Figure S52.  Get High-res Image Gene #33: 'del_6q16.3' versus Clinical Feature #13: 'BMI'

'del_6q16.3' versus 'COUNTRY_OF_ORIGIN'

P value = 0.00404 (Fisher's exact test), Q value = 0.1

Table S53.  Gene #33: 'del_6q16.3' 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
DEL PEAK 6(6Q16.3) MUTATED 2 0 11 0 1 1 0 0 11 31
DEL PEAK 6(6Q16.3) WILD-TYPE 0 1 7 1 1 1 1 3 22 14

Figure S53.  Get High-res Image Gene #33: 'del_6q16.3' versus Clinical Feature #16: 'COUNTRY_OF_ORIGIN'

'del_6q16.3' versus 'ORIGIN_ASIA'

P value = 0.000853 (Fisher's exact test), Q value = 0.044

Table S54.  Gene #33: 'del_6q16.3' versus Clinical Feature #17: 'ORIGIN_ASIA'

nPatients ASIAN WESTERN
ALL 63 45
DEL PEAK 6(6Q16.3) MUTATED 42 15
DEL PEAK 6(6Q16.3) WILD-TYPE 21 30

Figure S54.  Get High-res Image Gene #33: 'del_6q16.3' versus Clinical Feature #17: 'ORIGIN_ASIA'

'del_8p23.1' versus 'HISTOLOGIC_GRADE'

P value = 0.012 (Fisher's exact test), Q value = 0.17

Table S55.  Gene #34: 'del_8p23.1' versus Clinical Feature #3: 'HISTOLOGIC_GRADE'

nPatients G1 G2 G3 G4 GX
ALL 7 65 31 1 6
DEL PEAK 7(8P23.1) MUTATED 0 39 16 1 2
DEL PEAK 7(8P23.1) WILD-TYPE 7 26 15 0 4

Figure S55.  Get High-res Image Gene #34: 'del_8p23.1' versus Clinical Feature #3: 'HISTOLOGIC_GRADE'

'del_8p23.1' versus 'BMI'

P value = 0.00249 (Fisher's exact test), Q value = 0.083

Table S56.  Gene #34: 'del_8p23.1' versus Clinical Feature #13: 'BMI'

nPatients NORMAL OBESE OVERWEIGHT SEVERELY OBESE UNDERWEIGHT
ALL 53 10 28 3 16
DEL PEAK 7(8P23.1) MUTATED 33 6 6 2 11
DEL PEAK 7(8P23.1) WILD-TYPE 20 4 22 1 5

Figure S56.  Get High-res Image Gene #34: 'del_8p23.1' versus Clinical Feature #13: 'BMI'

'del_8p23.1' versus 'ORIGIN_ASIA'

P value = 0.0189 (Fisher's exact test), Q value = 0.21

Table S57.  Gene #34: 'del_8p23.1' versus Clinical Feature #17: 'ORIGIN_ASIA'

nPatients ASIAN WESTERN
ALL 63 45
DEL PEAK 7(8P23.1) MUTATED 39 17
DEL PEAK 7(8P23.1) WILD-TYPE 24 28

Figure S57.  Get High-res Image Gene #34: 'del_8p23.1' versus Clinical Feature #17: 'ORIGIN_ASIA'

'del_9p23' versus 'GENDER'

P value = 0.00202 (Fisher's exact test), Q value = 0.076

Table S58.  Gene #35: 'del_9p23' versus Clinical Feature #10: 'GENDER'

nPatients FEMALE MALE
ALL 37 73
DEL PEAK 8(9P23) MUTATED 29 34
DEL PEAK 8(9P23) WILD-TYPE 8 39

Figure S58.  Get High-res Image Gene #35: 'del_9p23' versus Clinical Feature #10: 'GENDER'

'del_9p21.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.0229 (Fisher's exact test), Q value = 0.24

Table S59.  Gene #36: 'del_9p21.3' versus Clinical Feature #2: 'HISTOLOGICAL_TYPE'

nPatients ACINAR ADENOCARCINOMA ADENOCARCINOMA BASALOID SQUAMOUS CELL CARCINOMA INVASIVE MUCINOUS ADENOCARCINOMA LEPIDIC ADENOCARCINOMA MICROPAPILLARY ADENOCARCINOMA OTHER PAPILLARY ADENOCARCINOMA SOLID ADENOCARCINOMA SQUAMOUS CELL CARCINOMA
ALL 13 68 1 3 1 2 7 5 8 2
DEL PEAK 9(9P21.3) MUTATED 8 41 1 0 1 1 7 4 2 2
DEL PEAK 9(9P21.3) WILD-TYPE 5 27 0 3 0 1 0 1 6 0

Figure S59.  Get High-res Image Gene #36: 'del_9p21.3' versus Clinical Feature #2: 'HISTOLOGICAL_TYPE'

'del_10q25.1' versus 'ORIGIN_ASIA'

P value = 0.0242 (Fisher's exact test), Q value = 0.24

Table S60.  Gene #37: 'del_10q25.1' versus Clinical Feature #17: 'ORIGIN_ASIA'

nPatients ASIAN WESTERN
ALL 63 45
DEL PEAK 10(10Q25.1) MUTATED 28 10
DEL PEAK 10(10Q25.1) WILD-TYPE 35 35

Figure S60.  Get High-res Image Gene #37: 'del_10q25.1' versus Clinical Feature #17: 'ORIGIN_ASIA'

'del_13q11' versus 'YEARS_TO_BIRTH'

P value = 0.00856 (Wilcoxon-test), Q value = 0.14

Table S61.  Gene #39: 'del_13q11' versus Clinical Feature #8: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 110 62.6 (9.6)
DEL PEAK 12(13Q11) MUTATED 64 60.7 (9.6)
DEL PEAK 12(13Q11) WILD-TYPE 46 65.3 (9.1)

Figure S61.  Get High-res Image Gene #39: 'del_13q11' versus Clinical Feature #8: 'YEARS_TO_BIRTH'

'del_13q11' versus 'BMI'

P value = 0.00434 (Fisher's exact test), Q value = 0.1

Table S62.  Gene #39: 'del_13q11' versus Clinical Feature #13: 'BMI'

nPatients NORMAL OBESE OVERWEIGHT SEVERELY OBESE UNDERWEIGHT
ALL 53 10 28 3 16
DEL PEAK 12(13Q11) MUTATED 34 4 10 2 14
DEL PEAK 12(13Q11) WILD-TYPE 19 6 18 1 2

Figure S62.  Get High-res Image Gene #39: 'del_13q11' versus Clinical Feature #13: 'BMI'

'del_13q11' versus 'COUNTRY_OF_ORIGIN'

P value = 1e-04 (Fisher's exact test), Q value = 0.017

Table S63.  Gene #39: 'del_13q11' 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
DEL PEAK 12(13Q11) MUTATED 2 0 11 0 0 1 1 1 11 36
DEL PEAK 12(13Q11) WILD-TYPE 0 1 7 1 2 1 0 2 22 9

Figure S63.  Get High-res Image Gene #39: 'del_13q11' versus Clinical Feature #16: 'COUNTRY_OF_ORIGIN'

'del_13q11' versus 'ORIGIN_ASIA'

P value = 6.72e-05 (Fisher's exact test), Q value = 0.015

Table S64.  Gene #39: 'del_13q11' versus Clinical Feature #17: 'ORIGIN_ASIA'

nPatients ASIAN WESTERN
ALL 63 45
DEL PEAK 12(13Q11) MUTATED 47 16
DEL PEAK 12(13Q11) WILD-TYPE 16 29

Figure S64.  Get High-res Image Gene #39: 'del_13q11' versus Clinical Feature #17: 'ORIGIN_ASIA'

'del_15q13.1' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0124 (Wilcoxon-test), Q value = 0.17

Table S65.  Gene #40: 'del_15q13.1' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 70 81.7 (9.0)
DEL PEAK 13(15Q13.1) MUTATED 46 79.8 (8.3)
DEL PEAK 13(15Q13.1) WILD-TYPE 24 85.4 (9.3)

Figure S65.  Get High-res Image Gene #40: 'del_15q13.1' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_15q13.1' versus 'SMOKER'

P value = 0.0173 (Fisher's exact test), Q value = 0.2

Table S66.  Gene #40: 'del_15q13.1' versus Clinical Feature #15: 'SMOKER'

nPatients NON-SMOKER SMOKER
ALL 46 61
DEL PEAK 13(15Q13.1) MUTATED 33 29
DEL PEAK 13(15Q13.1) WILD-TYPE 13 32

Figure S66.  Get High-res Image Gene #40: 'del_15q13.1' versus Clinical Feature #15: 'SMOKER'

'del_15q13.1' versus 'COUNTRY_OF_ORIGIN'

P value = 0.00593 (Fisher's exact test), Q value = 0.12

Table S67.  Gene #40: 'del_15q13.1' 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
DEL PEAK 13(15Q13.1) MUTATED 1 1 9 0 0 0 0 2 16 35
DEL PEAK 13(15Q13.1) WILD-TYPE 1 0 9 1 2 2 1 1 17 10

Figure S67.  Get High-res Image Gene #40: 'del_15q13.1' versus Clinical Feature #16: 'COUNTRY_OF_ORIGIN'

'del_15q13.1' versus 'ORIGIN_ASIA'

P value = 0.0101 (Fisher's exact test), Q value = 0.15

Table S68.  Gene #40: 'del_15q13.1' versus Clinical Feature #17: 'ORIGIN_ASIA'

nPatients ASIAN WESTERN
ALL 63 45
DEL PEAK 13(15Q13.1) MUTATED 44 20
DEL PEAK 13(15Q13.1) WILD-TYPE 19 25

Figure S68.  Get High-res Image Gene #40: 'del_15q13.1' versus Clinical Feature #17: 'ORIGIN_ASIA'

'del_17p13.1' versus 'BMI'

P value = 0.00635 (Fisher's exact test), Q value = 0.12

Table S69.  Gene #42: 'del_17p13.1' versus Clinical Feature #13: 'BMI'

nPatients NORMAL OBESE OVERWEIGHT SEVERELY OBESE UNDERWEIGHT
ALL 53 10 28 3 16
DEL PEAK 15(17P13.1) MUTATED 34 7 15 3 16
DEL PEAK 15(17P13.1) WILD-TYPE 19 3 13 0 0

Figure S69.  Get High-res Image Gene #42: 'del_17p13.1' versus Clinical Feature #13: 'BMI'

'del_18q21.31' versus 'BMI'

P value = 0.00023 (Fisher's exact test), Q value = 0.028

Table S70.  Gene #43: 'del_18q21.31' versus Clinical Feature #13: 'BMI'

nPatients NORMAL OBESE OVERWEIGHT SEVERELY OBESE UNDERWEIGHT
ALL 53 10 28 3 16
DEL PEAK 16(18Q21.31) MUTATED 32 5 8 1 15
DEL PEAK 16(18Q21.31) WILD-TYPE 21 5 20 2 1

Figure S70.  Get High-res Image Gene #43: 'del_18q21.31' versus Clinical Feature #13: 'BMI'

'del_18q21.31' versus 'COUNTRY_OF_ORIGIN'

P value = 0.0144 (Fisher's exact test), Q value = 0.19

Table S71.  Gene #43: 'del_18q21.31' 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
DEL PEAK 16(18Q21.31) MUTATED 1 1 10 0 0 1 0 0 14 32
DEL PEAK 16(18Q21.31) WILD-TYPE 1 0 8 1 2 1 1 3 19 13

Figure S71.  Get High-res Image Gene #43: 'del_18q21.31' versus Clinical Feature #16: 'COUNTRY_OF_ORIGIN'

'del_18q21.31' versus 'ORIGIN_ASIA'

P value = 0.00351 (Fisher's exact test), Q value = 0.096

Table S72.  Gene #43: 'del_18q21.31' versus Clinical Feature #17: 'ORIGIN_ASIA'

nPatients ASIAN WESTERN
ALL 63 45
DEL PEAK 16(18Q21.31) MUTATED 42 17
DEL PEAK 16(18Q21.31) WILD-TYPE 21 28

Figure S72.  Get High-res Image Gene #43: 'del_18q21.31' versus Clinical Feature #17: 'ORIGIN_ASIA'

'del_19q13.33' versus 'GENDER'

P value = 0.0125 (Fisher's exact test), Q value = 0.17

Table S73.  Gene #44: 'del_19q13.33' versus Clinical Feature #10: 'GENDER'

nPatients FEMALE MALE
ALL 37 73
DEL PEAK 17(19Q13.33) MUTATED 21 22
DEL PEAK 17(19Q13.33) WILD-TYPE 16 51

Figure S73.  Get High-res Image Gene #44: 'del_19q13.33' versus Clinical Feature #10: 'GENDER'

'del_21p11.2' versus 'GENDER'

P value = 0.00399 (Fisher's exact test), Q value = 0.1

Table S74.  Gene #45: 'del_21p11.2' versus Clinical Feature #10: 'GENDER'

nPatients FEMALE MALE
ALL 37 73
DEL PEAK 18(21P11.2) MUTATED 15 51
DEL PEAK 18(21P11.2) WILD-TYPE 22 22

Figure S74.  Get High-res Image Gene #45: 'del_21p11.2' versus Clinical Feature #10: 'GENDER'

'del_22p11.2' versus 'HISTOLOGICAL_TYPE'

P value = 0.00584 (Fisher's exact test), Q value = 0.12

Table S75.  Gene #47: 'del_22p11.2' versus Clinical Feature #2: 'HISTOLOGICAL_TYPE'

nPatients ACINAR ADENOCARCINOMA ADENOCARCINOMA BASALOID SQUAMOUS CELL CARCINOMA INVASIVE MUCINOUS ADENOCARCINOMA LEPIDIC ADENOCARCINOMA MICROPAPILLARY ADENOCARCINOMA OTHER PAPILLARY ADENOCARCINOMA SOLID ADENOCARCINOMA SQUAMOUS CELL CARCINOMA
ALL 13 68 1 3 1 2 7 5 8 2
DEL PEAK 20(22P11.2) MUTATED 1 29 0 2 1 0 2 1 7 1
DEL PEAK 20(22P11.2) WILD-TYPE 12 39 1 1 0 2 5 4 1 1

Figure S75.  Get High-res Image Gene #47: 'del_22p11.2' versus Clinical Feature #2: 'HISTOLOGICAL_TYPE'

'del_22p11.2' versus 'GENDER'

P value = 0.0231 (Fisher's exact test), Q value = 0.24

Table S76.  Gene #47: 'del_22p11.2' versus Clinical Feature #10: 'GENDER'

nPatients FEMALE MALE
ALL 37 73
DEL PEAK 20(22P11.2) MUTATED 9 35
DEL PEAK 20(22P11.2) WILD-TYPE 28 38

Figure S76.  Get High-res Image Gene #47: 'del_22p11.2' versus Clinical Feature #10: 'GENDER'

'del_22p11.2' versus 'RADIATION_THERAPY'

P value = 0.0112 (Fisher's exact test), Q value = 0.16

Table S77.  Gene #47: 'del_22p11.2' versus Clinical Feature #12: 'RADIATION_THERAPY'

nPatients NO YES
ALL 71 22
DEL PEAK 20(22P11.2) MUTATED 20 13
DEL PEAK 20(22P11.2) WILD-TYPE 51 9

Figure S77.  Get High-res Image Gene #47: 'del_22p11.2' versus Clinical Feature #12: 'RADIATION_THERAPY'

'del_22p11.2' versus 'COUNTRY_OF_ORIGIN'

P value = 0.00956 (Fisher's exact test), Q value = 0.15

Table S78.  Gene #47: 'del_22p11.2' 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
DEL PEAK 20(22P11.2) MUTATED 2 0 7 0 0 0 1 1 7 25
DEL PEAK 20(22P11.2) WILD-TYPE 0 1 11 1 2 2 0 2 26 20

Figure S78.  Get High-res Image Gene #47: 'del_22p11.2' versus Clinical Feature #16: 'COUNTRY_OF_ORIGIN'

'del_22p11.2' versus 'ORIGIN_ASIA'

P value = 0.00916 (Fisher's exact test), Q value = 0.15

Table S79.  Gene #47: 'del_22p11.2' versus Clinical Feature #17: 'ORIGIN_ASIA'

nPatients ASIAN WESTERN
ALL 63 45
DEL PEAK 20(22P11.2) MUTATED 32 11
DEL PEAK 20(22P11.2) WILD-TYPE 31 34

Figure S79.  Get High-res Image Gene #47: 'del_22p11.2' versus Clinical Feature #17: 'ORIGIN_ASIA'

'del_22q13.32' versus 'BMI'

P value = 0.00743 (Fisher's exact test), Q value = 0.13

Table S80.  Gene #48: 'del_22q13.32' versus Clinical Feature #13: 'BMI'

nPatients NORMAL OBESE OVERWEIGHT SEVERELY OBESE UNDERWEIGHT
ALL 53 10 28 3 16
DEL PEAK 21(22Q13.32) MUTATED 31 7 6 2 9
DEL PEAK 21(22Q13.32) WILD-TYPE 22 3 22 1 7

Figure S80.  Get High-res Image Gene #48: 'del_22q13.32' versus Clinical Feature #13: 'BMI'

'del_22q13.32' versus 'COUNTRY_OF_ORIGIN'

P value = 0.016 (Fisher's exact test), Q value = 0.2

Table S81.  Gene #48: 'del_22q13.32' 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
DEL PEAK 21(22Q13.32) MUTATED 2 1 9 0 0 1 1 1 10 29
DEL PEAK 21(22Q13.32) WILD-TYPE 0 0 9 1 2 1 0 2 23 16

Figure S81.  Get High-res Image Gene #48: 'del_22q13.32' versus Clinical Feature #16: 'COUNTRY_OF_ORIGIN'

'del_22q13.32' versus 'ORIGIN_ASIA'

P value = 0.0187 (Fisher's exact test), Q value = 0.21

Table S82.  Gene #48: 'del_22q13.32' versus Clinical Feature #17: 'ORIGIN_ASIA'

nPatients ASIAN WESTERN
ALL 63 45
DEL PEAK 21(22Q13.32) MUTATED 38 16
DEL PEAK 21(22Q13.32) WILD-TYPE 25 29

Figure S82.  Get High-res Image Gene #48: 'del_22q13.32' versus Clinical Feature #17: 'ORIGIN_ASIA'

'del_xp22.33' versus 'GENDER'

P value = 0.000859 (Fisher's exact test), Q value = 0.044

Table S83.  Gene #49: 'del_xp22.33' versus Clinical Feature #10: 'GENDER'

nPatients FEMALE MALE
ALL 37 73
DEL PEAK 22(XP22.33) MUTATED 15 8
DEL PEAK 22(XP22.33) WILD-TYPE 22 65

Figure S83.  Get High-res Image Gene #49: 'del_xp22.33' versus Clinical Feature #10: 'GENDER'

'del_xq28' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00195 (Wilcoxon-test), Q value = 0.076

Table S84.  Gene #50: 'del_xq28' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 70 81.7 (9.0)
DEL PEAK 23(XQ28) MUTATED 18 76.1 (6.1)
DEL PEAK 23(XQ28) WILD-TYPE 52 83.7 (9.1)

Figure S84.  Get High-res Image Gene #50: 'del_xq28' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_xq28' versus 'COUNTRY_OF_ORIGIN'

P value = 0.00397 (Fisher's exact test), Q value = 0.1

Table S85.  Gene #50: 'del_xq28' 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
DEL PEAK 23(XQ28) MUTATED 0 0 0 0 1 0 0 2 4 17
DEL PEAK 23(XQ28) WILD-TYPE 2 1 18 1 1 2 1 1 29 28

Figure S85.  Get High-res Image Gene #50: 'del_xq28' versus Clinical Feature #16: 'COUNTRY_OF_ORIGIN'

'del_yq11.223' versus 'PATHOLOGIC_STAGE'

P value = 0.00823 (Fisher's exact test), Q value = 0.14

Table S86.  Gene #51: 'del_yq11.223' 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
DEL PEAK 24(YQ11.223) MUTATED 1 14 29 10 7 0 8 0
DEL PEAK 24(YQ11.223) WILD-TYPE 1 8 5 7 6 1 12 1

Figure S86.  Get High-res Image Gene #51: 'del_yq11.223' versus Clinical Feature #7: 'PATHOLOGIC_STAGE'

Methods & Data
Input

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

  • Processed Copy number data file = /cromwell_root/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a/5f3cf94d-1fd8-4096-b606-bcdd9599f833/correlate_genomic_events_all/3441da4a-c848-4650-95a4-60c86ad83a57/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 focal cnvs = 51

  • Number of selected clinical features = 17

  • 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

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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