Correlation between copy number variation genes (focal events) and selected clinical features
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 36 focal events and 17 clinical features across 499 patients, 38 significant findings detected with Q value < 0.25.

  • amp_1q31.2 cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'HISTOLOGICAL_TYPE',  'EXTRATHYROIDAL_EXTENSION',  'TUMOR_SIZE', and 'RACE'.

  • amp_4q31.21 cnv correlated to 'NUMBER_OF_LYMPH_NODES'.

  • amp_5q21.1 cnv correlated to 'PATHOLOGIC_STAGE' and 'NUMBER_OF_LYMPH_NODES'.

  • amp_5q33.1 cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGIC_STAGE', and 'NUMBER_OF_LYMPH_NODES'.

  • amp_22q11.21 cnv correlated to 'RESIDUAL_TUMOR'.

  • amp_xq22.3 cnv correlated to 'GENDER' and 'EXTRATHYROIDAL_EXTENSION'.

  • del_2p23.1 cnv correlated to 'HISTOLOGICAL_TYPE' and 'NUMBER_OF_LYMPH_NODES'.

  • del_2q22.1 cnv correlated to 'PATHOLOGY_N_STAGE',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • del_2q37.3 cnv correlated to 'PATHOLOGIC_STAGE' and 'NUMBER_OF_LYMPH_NODES'.

  • del_9p21.3 cnv correlated to 'YEARS_TO_BIRTH' and 'PATHOLOGIC_STAGE'.

  • del_9q22.33 cnv correlated to 'YEARS_TO_BIRTH' and 'PATHOLOGIC_STAGE'.

  • del_10q23.31 cnv correlated to 'TUMOR_SIZE'.

  • del_13q12.3 cnv correlated to 'YEARS_TO_BIRTH' and 'RADIATION_EXPOSURE'.

  • del_13q14.3 cnv correlated to 'RADIATION_EXPOSURE'.

  • del_16q23.3 cnv correlated to 'PATHOLOGIC_STAGE'.

  • del_17p13.1 cnv correlated to 'TUMOR_SIZE'.

  • del_19p13.2 cnv correlated to 'TUMOR_SIZE'.

  • del_19p13.12 cnv correlated to 'TUMOR_SIZE'.

  • del_21q21.1 cnv correlated to 'PATHOLOGIC_STAGE'.

  • del_xq28 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 36 focal events and 17 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 38 significant findings detected.

Clinical
Features 		Time
to
Death 		YEARS
TO
BIRTH 		PATHOLOGIC
STAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER RADIATION
THERAPY 		HISTOLOGICAL
TYPE 		RADIATION
EXPOSURE 		EXTRATHYROIDAL
EXTENSION 		RESIDUAL
TUMOR 		NUMBER
OF
LYMPH
NODES 		MULTIFOCALITY TUMOR
SIZE 		RACE ETHNICITY
nCNV (%) nWild-Type logrank test Wilcoxon-test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Wilcoxon-test Fisher's exact test Wilcoxon-test Fisher's exact test Fisher's exact test
amp 1q31 2 29 (6%) 470 0.234
(0.775) 		5.12e-05
(0.00783) 		1e-05
(0.00408) 		2e-05
(0.00408) 		0.000629
(0.0482) 		1
(1.00) 		0.666
(1.00) 		0.303
(0.87) 		0.00601
(0.175) 		1
(1.00) 		2e-05
(0.00408) 		0.0423
(0.364) 		0.0293
(0.31) 		0.124
(0.574) 		0.00305
(0.111) 		0.00327
(0.111) 		0.0279
(0.299)
amp 5q33 1 21 (4%) 478 0.0358
(0.348) 		0.0131
(0.236) 		0.00338
(0.111) 		0.556
(1.00) 		0.0191
(0.266) 		1
(1.00) 		0.312
(0.879) 		0.465
(1.00) 		0.0901
(0.487) 		1
(1.00) 		0.0278
(0.299) 		0.395
(0.971) 		0.01
(0.214) 		1
(1.00) 		0.0825
(0.462) 		1
(1.00) 		0.623
(1.00)
del 2q22 1 10 (2%) 489 0.619
(1.00) 		0.264
(0.823) 		0.0253
(0.299) 		0.797
(1.00) 		0.0149
(0.246) 		1
(1.00) 		0.732
(1.00) 		0.495
(1.00) 		0.00482
(0.147) 		1
(1.00) 		0.15
(0.646) 		0.455
(1.00) 		0.00663
(0.178) 		1
(1.00) 		0.349
(0.925) 		1
(1.00) 		1
(1.00)
amp 5q21 1 23 (5%) 476 0.081
(0.462) 		0.022
(0.282) 		0.00793
(0.187) 		0.706
(1.00) 		0.0168
(0.254) 		1
(1.00) 		0.226
(0.775) 		0.809
(1.00) 		0.338
(0.905) 		1
(1.00) 		0.0477
(0.369) 		0.41
(0.989) 		0.00793
(0.187) 		0.834
(1.00) 		0.165
(0.687) 		0.222
(0.775) 		1
(1.00)
amp xq22 3 15 (3%) 484 0.16
(0.673) 		0.375
(0.964) 		0.181
(0.7) 		0.576
(1.00) 		0.416
(1) 		1
(1.00) 		0.0147
(0.246) 		0.566
(1.00) 		0.496
(1.00) 		1
(1.00) 		0.0101
(0.214) 		0.791
(1.00) 		0.308
(0.879) 		0.302
(0.87) 		0.77
(1.00) 		0.8
(1.00) 		1
(1.00)
del 2p23 1 12 (2%) 487 0.619
(1.00) 		0.711
(1.00) 		0.0452
(0.364) 		0.868
(1.00) 		0.0201
(0.268) 		1
(1.00) 		0.742
(1.00) 		1
(1.00) 		0.0027
(0.111) 		1
(1.00) 		0.0756
(0.446) 		0.45
(1.00) 		0.0109
(0.216) 		0.779
(1.00) 		0.931
(1.00) 		1
(1.00) 		1
(1.00)
del 2q37 3 13 (3%) 486 0.236
(0.775) 		0.139
(0.611) 		0.0128
(0.236) 		0.449
(1.00) 		0.0372
(0.356) 		1
(1.00) 		0.349
(0.925) 		0.548
(1.00) 		0.0443
(0.364) 		0.383
(0.964) 		0.236
(0.775) 		0.234
(0.775) 		0.0155
(0.25) 		0.779
(1.00) 		0.0524
(0.377) 		0.759
(1.00) 		1
(1.00)
del 9p21 3 20 (4%) 479 0.049
(0.369) 		0.00966
(0.214) 		0.00023
(0.0282) 		0.177
(0.69) 		1
(1.00) 		0.202
(0.753) 		0.441
(1.00) 		0.465
(1.00) 		0.621
(1.00) 		1
(1.00) 		0.0601
(0.394) 		0.479
(1.00) 		0.123
(0.574) 		0.172
(0.69) 		0.105
(0.549) 		0.888
(1.00) 		0.379
(0.964)
del 9q22 33 27 (5%) 472 0.0642
(0.406) 		0.000623
(0.0482) 		0.00035
(0.0357) 		0.116
(0.572) 		0.294
(0.868) 		0.3
(0.87) 		0.503
(1.00) 		0.669
(1.00) 		1
(1.00) 		1
(1.00) 		0.0908
(0.487) 		0.824
(1.00) 		0.901
(1.00) 		0.692
(1.00) 		0.0189
(0.266) 		0.83
(1.00) 		1
(1.00)
del 13q12 3 16 (3%) 483 0.0274
(0.299) 		0.00132
(0.0805) 		0.121
(0.574) 		0.896
(1.00) 		0.0876
(0.479) 		1
(1.00) 		0.15
(0.646) 		0.0592
(0.394) 		0.49
(1.00) 		0.00166
(0.0922) 		0.78
(1.00) 		0.791
(1.00) 		0.137
(0.608) 		0.802
(1.00) 		0.238
(0.775) 		0.863
(1.00) 		0.615
(1.00)
amp 4q31 21 9 (2%) 490 0.221
(0.775) 		0.0396
(0.364) 		0.257
(0.809) 		0.637
(1.00) 		0.0679
(0.415) 		1
(1.00) 		1
(1.00) 		0.676
(1.00) 		0.547
(1.00) 		1
(1.00) 		0.805
(1.00) 		0.637
(1.00) 		0.0108
(0.216) 		0.313
(0.879) 		0.116
(0.572) 		0.0179
(0.261) 		1
(1.00)
amp 22q11 21 7 (1%) 492 0.785
(1.00) 		0.817
(1.00) 		0.224
(0.775) 		0.614
(1.00) 		1
(1.00) 		1
(1.00) 		0.198
(0.742) 		1
(1.00) 		0.372
(0.961) 		1
(1.00) 		0.748
(1.00) 		0.0127
(0.236) 		0.693
(1.00) 		1
(1.00) 		0.213
(0.775) 		0.317
(0.882) 		0.396
(0.971)
del 10q23 31 12 (2%) 487 0.568
(1.00) 		0.206
(0.762) 		0.0445
(0.364) 		0.765
(1.00) 		0.0201
(0.268) 		1
(1.00) 		0.319
(0.885) 		0.754
(1.00) 		0.327
(0.898) 		1
(1.00) 		0.708
(1.00) 		0.623
(1.00) 		0.0273
(0.299) 		1
(1.00) 		0.00234
(0.11) 		1
(1.00) 		1
(1.00)
del 13q14 3 20 (4%) 479 0.0445
(0.364) 		0.0457
(0.364) 		0.616
(1.00) 		0.968
(1.00) 		0.0449
(0.364) 		1
(1.00) 		0.441
(1.00) 		0.468
(1.00) 		0.532
(1.00) 		0.00345
(0.111) 		0.404
(0.982) 		0.76
(1.00) 		0.083
(0.462) 		0.494
(1.00) 		0.24
(0.775) 		1
(1.00) 		1
(1.00)
del 16q23 3 6 (1%) 493 0.186
(0.71) 		0.0506
(0.373) 		0.00215
(0.11) 		0.0163
(0.254) 		0.449
(1.00) 		0.12
(0.574) 		1
(1.00) 		0.419
(1.00) 		0.175
(0.69) 		0.213
(0.775) 		0.0644
(0.406) 		0.0729
(0.442) 		0.856
(1.00) 		1
(1.00) 		0.42
(1.00) 		0.473
(1.00) 		1
(1.00)
del 17p13 1 8 (2%) 491 0.575
(1.00) 		0.901
(1.00) 		0.147
(0.643) 		0.0312
(0.313) 		0.724
(1.00) 		1
(1.00) 		1
(1.00) 		0.478
(1.00) 		0.222
(0.775) 		0.274
(0.83) 		0.06
(0.394) 		0.339
(0.905) 		0.909
(1.00) 		0.731
(1.00) 		0.0141
(0.246) 		0.582
(1.00) 		1
(1.00)
del 19p13 2 7 (1%) 492 0.129
(0.596) 		0.166
(0.687) 		0.495
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.392
(0.971) 		0.715
(1.00) 		1
(1.00) 		0.0267
(0.299) 		1
(1.00) 		0.187
(0.71) 		0.46
(1.00) 		0.00278
(0.111) 		0.759
(1.00) 		1
(1.00)
del 19p13 12 8 (2%) 491 0.1
(0.53) 		0.263
(0.823) 		0.267
(0.826) 		0.881
(1.00) 		0.623
(1.00) 		1
(1.00) 		0.448
(1.00) 		1
(1.00) 		1
(1.00) 		0.0267
(0.299) 		0.601
(1.00) 		0.281
(0.846) 		1
(1.00) 		0.00769
(0.187) 		0.137
(0.608) 		1
(1.00)
del 21q21 1 9 (2%) 490 0.686
(1.00) 		0.107
(0.553) 		0.00669
(0.178) 		0.265
(0.823) 		1
(1.00) 		1
(1.00) 		0.707
(1.00) 		1
(1.00) 		0.643
(1.00) 		1
(1.00) 		0.622
(1.00) 		0.398
(0.971) 		0.736
(1.00) 		0.313
(0.879) 		0.465
(1.00) 		0.296
(0.868) 		1
(1.00)
del xq28 4 (1%) 495 0.753
(1.00) 		0.223
(0.775) 		0.00098
(0.0666) 		0.0483
(0.369) 		0.123
(0.574) 		0.0611
(0.394) 		0.302
(0.87) 		1
(1.00) 		0.112
(0.572) 		0.644
(1.00) 		0.31
(0.879) 		0.041
(0.364) 		1
(1.00) 		0.656
(1.00) 		1
(1.00)
amp 13q14 2 6 (1%) 493 0.744
(1.00) 		0.476
(1.00) 		0.118
(0.572) 		0.705
(1.00) 		0.372
(0.961) 		1
(1.00) 		1
(1.00) 		0.676
(1.00) 		0.232
(0.775) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.041
(0.364) 		1
(1.00) 		0.91
(1.00) 		0.48
(1.00) 		1
(1.00)
amp xp11 22 8 (2%) 491 0.0583
(0.394) 		0.0495
(0.369) 		0.0307
(0.313) 		0.398
(0.971) 		0.449
(1.00) 		1
(1.00) 		0.688
(1.00) 		1
(1.00) 		0.222
(0.775) 		0.274
(0.83) 		0.0255
(0.299) 		0.238
(0.775) 		0.117
(0.572) 		0.48
(1.00) 		0.177
(0.69) 		0.666
(1.00) 		1
(1.00)
del 1q42 13 5 (1%) 494 0.575
(1.00) 		0.461
(1.00) 		0.793
(1.00) 		0.517
(1.00) 		0.623
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.555
(1.00) 		1
(1.00) 		1
(1.00) 		0.635
(1.00) 		0.392
(0.971) 		1
(1.00) 		0.0423
(0.364) 		1
(1.00) 		0.0471
(0.369)
del 4q34 3 5 (1%) 494 0.602
(1.00) 		0.742
(1.00) 		0.115
(0.572) 		0.174
(0.69) 		0.623
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.554
(1.00) 		1
(1.00) 		0.135
(0.608) 		1
(1.00) 		0.289
(0.863) 		0.38
(0.964) 		0.0533
(0.379) 		0.58
(1.00) 		1
(1.00)
del 5p15 2 4 (1%) 495 0.86
(1.00) 		0.182
(0.702) 		0.226
(0.775) 		0.631
(1.00) 		0.372
(0.961) 		1
(1.00) 		0.578
(1.00) 		0.631
(1.00) 		0.223
(0.775) 		1
(1.00) 		0.425
(1.00) 		0.0677
(0.415) 		0.865
(1.00) 		0.338
(0.905) 		0.21
(0.774) 		0.316
(0.882) 		0.332
(0.904)
del 7q34 4 (1%) 495 0.713
(1.00) 		0.757
(1.00) 		0.47
(1.00) 		0.503
(1.00) 		0.623
(1.00) 		1
(1.00) 		1
(1.00) 		0.631
(1.00) 		0.132
(0.602) 		1
(1.00) 		0.644
(1.00) 		1
(1.00) 		0.47
(1.00) 		0.628
(1.00) 		0.0875
(0.479) 		1
(1.00) 		1
(1.00)
del 8p23 2 4 (1%) 495 0.82
(1.00) 		0.913
(1.00) 		0.173
(0.69) 		0.872
(1.00) 		0.248
(0.787) 		1
(1.00) 		0.0611
(0.394) 		0.631
(1.00) 		0.452
(1.00) 		1
(1.00) 		0.645
(1.00) 		1
(1.00) 		0.0773
(0.446) 		1
(1.00) 		0.737
(1.00) 		1
(1.00)
del 8p22 4 (1%) 495 0.82
(1.00) 		0.913
(1.00) 		0.171
(0.69) 		0.871
(1.00) 		0.248
(0.787) 		1
(1.00) 		0.0611
(0.394) 		0.631
(1.00) 		0.45
(1.00) 		1
(1.00) 		0.644
(1.00) 		1
(1.00) 		0.0773
(0.446) 		1
(1.00) 		0.737
(1.00) 		1
(1.00)
del 8p12 4 (1%) 495 0.82
(1.00) 		0.913
(1.00) 		0.171
(0.69) 		0.871
(1.00) 		0.248
(0.787) 		1
(1.00) 		0.0611
(0.394) 		0.631
(1.00) 		0.451
(1.00) 		1
(1.00) 		0.642
(1.00) 		1
(1.00) 		0.0773
(0.446) 		1
(1.00) 		0.737
(1.00) 		1
(1.00)
del 8q24 22 7 (1%) 492 0.754
(1.00) 		0.409
(0.989) 		0.113
(0.572) 		0.796
(1.00) 		0.0611
(0.394) 		1
(1.00) 		0.017
(0.254) 		0.433
(1.00) 		0.152
(0.649) 		1
(1.00) 		0.758
(1.00) 		0.524
(1.00) 		0.041
(0.364) 		1
(1.00) 		0.27
(0.83) 		1
(1.00) 		1
(1.00)
del 10p12 31 7 (1%) 492 0.626
(1.00) 		0.59
(1.00) 		0.382
(0.964) 		0.74
(1.00) 		0.0302
(0.313) 		1
(1.00) 		0.392
(0.971) 		1
(1.00) 		0.816
(1.00) 		1
(1.00) 		0.757
(1.00) 		1
(1.00) 		0.0221
(0.282) 		0.708
(1.00) 		0.0818
(0.462) 		0.732
(1.00) 		1
(1.00)
del 10q21 2 12 (2%) 487 0.571
(1.00) 		0.971
(1.00) 		0.828
(1.00) 		0.741
(1.00) 		0.338
(0.905) 		1
(1.00) 		0.742
(1.00) 		0.754
(1.00) 		0.531
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.352
(0.928) 		0.761
(1.00) 		0.0352
(0.348) 		0.842
(1.00) 		0.61
(1.00)
del 15q25 3 8 (2%) 491 0.574
(1.00) 		0.754
(1.00) 		0.241
(0.775) 		0.73
(1.00) 		0.122
(0.574) 		0.0915
(0.487) 		0.688
(1.00) 		1
(1.00) 		0.0458
(0.364) 		1
(1.00) 		0.601
(1.00) 		0.786
(1.00) 		0.135
(0.608) 		0.731
(1.00) 		0.0758
(0.446) 		0.666
(1.00) 		0.396
(0.971)
del 18q21 33 5 (1%) 494 0.61
(1.00) 		0.36
(0.946) 		0.232
(0.775) 		0.155
(0.661) 		0.623
(1.00) 		1
(1.00) 		1
(1.00) 		0.366
(0.958) 		0.553
(1.00) 		1
(1.00) 		0.453
(1.00) 		1
(1.00) 		0.174
(0.69) 		0.38
(0.964) 		0.838
(1.00) 		1
(1.00) 		0.0251
(0.299)
del 22q13 1 89 (18%) 410 0.238
(0.775) 		0.458
(1.00) 		0.679
(1.00) 		0.861
(1.00) 		0.326
(0.898) 		0.644
(1.00) 		0.43
(1.00) 		0.0673
(0.415) 		0.162
(0.68) 		0.332
(0.904) 		0.551
(1.00) 		0.295
(0.868) 		0.513
(1.00) 		0.286
(0.857) 		0.579
(1.00) 		0.431
(1.00) 		1
(1.00)
del 22q13 32 90 (18%) 409 0.237
(0.775) 		0.487
(1.00) 		0.7
(1.00) 		0.888
(1.00) 		0.272
(0.83) 		0.649
(1.00) 		0.511
(1.00) 		0.0523
(0.377) 		0.116
(0.572) 		0.218
(0.775) 		0.483
(1.00) 		0.294
(0.868) 		0.433
(1.00) 		0.197
(0.742) 		0.579
(1.00) 		0.455
(1.00) 		1
(1.00)
'amp_1q31.2' versus 'YEARS_TO_BIRTH'

P value = 5.12e-05 (Wilcoxon-test), Q value = 0.0078

Table S1.  Gene #1: 'amp_1q31.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 499 47.3 (15.8)
AMP PEAK 1(1Q31.2) MUTATED 29 59.9 (17.3)
AMP PEAK 1(1Q31.2) WILD-TYPE 470 46.5 (15.3)

Figure S1.  Get High-res Image Gene #1: 'amp_1q31.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_1q31.2' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0041

Table S2.  Gene #1: 'amp_1q31.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
ALL 282 50 111 2 46 6
AMP PEAK 1(1Q31.2) MUTATED 7 0 12 1 9 0
AMP PEAK 1(1Q31.2) WILD-TYPE 275 50 99 1 37 6

Figure S2.  Get High-res Image Gene #1: 'amp_1q31.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'amp_1q31.2' versus 'PATHOLOGY_T_STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.0041

Table S3.  Gene #1: 'amp_1q31.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 142 165 167 23
AMP PEAK 1(1Q31.2) MUTATED 2 4 18 5
AMP PEAK 1(1Q31.2) WILD-TYPE 140 161 149 18

Figure S3.  Get High-res Image Gene #1: 'amp_1q31.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_1q31.2' versus 'PATHOLOGY_N_STAGE'

P value = 0.000629 (Fisher's exact test), Q value = 0.048

Table S4.  Gene #1: 'amp_1q31.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 225 224
AMP PEAK 1(1Q31.2) MUTATED 5 22
AMP PEAK 1(1Q31.2) WILD-TYPE 220 202

Figure S4.  Get High-res Image Gene #1: 'amp_1q31.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_1q31.2' versus 'HISTOLOGICAL_TYPE'

P value = 0.00601 (Fisher's exact test), Q value = 0.18

Table S5.  Gene #1: 'amp_1q31.2' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients OTHER, SPECIFY THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED) THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
ALL 7 356 100 36
AMP PEAK 1(1Q31.2) MUTATED 0 25 0 4
AMP PEAK 1(1Q31.2) WILD-TYPE 7 331 100 32

Figure S5.  Get High-res Image Gene #1: 'amp_1q31.2' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_1q31.2' versus 'EXTRATHYROIDAL_EXTENSION'

P value = 2e-05 (Fisher's exact test), Q value = 0.0041

Table S6.  Gene #1: 'amp_1q31.2' versus Clinical Feature #11: 'EXTRATHYROIDAL_EXTENSION'

nPatients MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE VERY ADVANCED (T4B)
ALL 132 18 330 1
AMP PEAK 1(1Q31.2) MUTATED 14 4 10 1
AMP PEAK 1(1Q31.2) WILD-TYPE 118 14 320 0

Figure S6.  Get High-res Image Gene #1: 'amp_1q31.2' versus Clinical Feature #11: 'EXTRATHYROIDAL_EXTENSION'

'amp_1q31.2' versus 'TUMOR_SIZE'

P value = 0.00305 (Wilcoxon-test), Q value = 0.11

Table S7.  Gene #1: 'amp_1q31.2' versus Clinical Feature #15: 'TUMOR_SIZE'

nPatients Mean (Std.Dev)
ALL 401 3.0 (1.6)
AMP PEAK 1(1Q31.2) MUTATED 24 3.8 (1.5)
AMP PEAK 1(1Q31.2) WILD-TYPE 377 2.9 (1.6)

Figure S7.  Get High-res Image Gene #1: 'amp_1q31.2' versus Clinical Feature #15: 'TUMOR_SIZE'

'amp_1q31.2' versus 'RACE'

P value = 0.00327 (Fisher's exact test), Q value = 0.11

Table S8.  Gene #1: 'amp_1q31.2' versus Clinical Feature #16: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 52 27 329
AMP PEAK 1(1Q31.2) MUTATED 1 1 5 21
AMP PEAK 1(1Q31.2) WILD-TYPE 0 51 22 308

Figure S8.  Get High-res Image Gene #1: 'amp_1q31.2' versus Clinical Feature #16: 'RACE'

'amp_4q31.21' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0108 (Wilcoxon-test), Q value = 0.22

Table S9.  Gene #2: 'amp_4q31.21' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 386 3.6 (6.0)
AMP PEAK 3(4Q31.21) MUTATED 8 0.1 (0.4)
AMP PEAK 3(4Q31.21) WILD-TYPE 378 3.6 (6.0)

Figure S9.  Get High-res Image Gene #2: 'amp_4q31.21' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'amp_5q21.1' versus 'PATHOLOGIC_STAGE'

P value = 0.00793 (Fisher's exact test), Q value = 0.19

Table S10.  Gene #3: 'amp_5q21.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
ALL 282 50 111 2 46 6
AMP PEAK 4(5Q21.1) MUTATED 8 7 5 1 2 0
AMP PEAK 4(5Q21.1) WILD-TYPE 274 43 106 1 44 6

Figure S10.  Get High-res Image Gene #3: 'amp_5q21.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'amp_5q21.1' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00793 (Wilcoxon-test), Q value = 0.19

Table S11.  Gene #3: 'amp_5q21.1' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 386 3.6 (6.0)
AMP PEAK 4(5Q21.1) MUTATED 15 0.8 (1.9)
AMP PEAK 4(5Q21.1) WILD-TYPE 371 3.7 (6.1)

Figure S11.  Get High-res Image Gene #3: 'amp_5q21.1' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'amp_5q33.1' versus 'YEARS_TO_BIRTH'

P value = 0.0131 (Wilcoxon-test), Q value = 0.24

Table S12.  Gene #4: 'amp_5q33.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 499 47.3 (15.8)
AMP PEAK 5(5Q33.1) MUTATED 21 55.7 (14.8)
AMP PEAK 5(5Q33.1) WILD-TYPE 478 46.9 (15.7)

Figure S12.  Get High-res Image Gene #4: 'amp_5q33.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_5q33.1' versus 'PATHOLOGIC_STAGE'

P value = 0.00338 (Fisher's exact test), Q value = 0.11

Table S13.  Gene #4: 'amp_5q33.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
ALL 282 50 111 2 46 6
AMP PEAK 5(5Q33.1) MUTATED 7 7 5 1 1 0
AMP PEAK 5(5Q33.1) WILD-TYPE 275 43 106 1 45 6

Figure S13.  Get High-res Image Gene #4: 'amp_5q33.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'amp_5q33.1' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.01 (Wilcoxon-test), Q value = 0.21

Table S14.  Gene #4: 'amp_5q33.1' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 386 3.6 (6.0)
AMP PEAK 5(5Q33.1) MUTATED 14 1.4 (3.8)
AMP PEAK 5(5Q33.1) WILD-TYPE 372 3.6 (6.0)

Figure S14.  Get High-res Image Gene #4: 'amp_5q33.1' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'amp_22q11.21' versus 'RESIDUAL_TUMOR'

P value = 0.0127 (Fisher's exact test), Q value = 0.24

Table S15.  Gene #6: 'amp_22q11.21' versus Clinical Feature #12: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 383 51 4 30
AMP PEAK 7(22Q11.21) MUTATED 2 2 0 2
AMP PEAK 7(22Q11.21) WILD-TYPE 381 49 4 28

Figure S15.  Get High-res Image Gene #6: 'amp_22q11.21' versus Clinical Feature #12: 'RESIDUAL_TUMOR'

'amp_xq22.3' versus 'GENDER'

P value = 0.0147 (Fisher's exact test), Q value = 0.25

Table S16.  Gene #8: 'amp_xq22.3' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 365 134
AMP PEAK 9(XQ22.3) MUTATED 15 0
AMP PEAK 9(XQ22.3) WILD-TYPE 350 134

Figure S16.  Get High-res Image Gene #8: 'amp_xq22.3' versus Clinical Feature #7: 'GENDER'

'amp_xq22.3' versus 'EXTRATHYROIDAL_EXTENSION'

P value = 0.0101 (Fisher's exact test), Q value = 0.21

Table S17.  Gene #8: 'amp_xq22.3' versus Clinical Feature #11: 'EXTRATHYROIDAL_EXTENSION'

nPatients MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE VERY ADVANCED (T4B)
ALL 132 18 330 1
AMP PEAK 9(XQ22.3) MUTATED 1 0 13 1
AMP PEAK 9(XQ22.3) WILD-TYPE 131 18 317 0

Figure S17.  Get High-res Image Gene #8: 'amp_xq22.3' versus Clinical Feature #11: 'EXTRATHYROIDAL_EXTENSION'

'del_2p23.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.0027 (Fisher's exact test), Q value = 0.11

Table S18.  Gene #10: 'del_2p23.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients OTHER, SPECIFY THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED) THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
ALL 7 356 100 36
DEL PEAK 2(2P23.1) MUTATED 1 4 7 0
DEL PEAK 2(2P23.1) WILD-TYPE 6 352 93 36

Figure S18.  Get High-res Image Gene #10: 'del_2p23.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_2p23.1' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0109 (Wilcoxon-test), Q value = 0.22

Table S19.  Gene #10: 'del_2p23.1' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 386 3.6 (6.0)
DEL PEAK 2(2P23.1) MUTATED 9 0.3 (1.0)
DEL PEAK 2(2P23.1) WILD-TYPE 377 3.6 (6.0)

Figure S19.  Get High-res Image Gene #10: 'del_2p23.1' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'del_2q22.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.0149 (Fisher's exact test), Q value = 0.25

Table S20.  Gene #11: 'del_2q22.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 225 224
DEL PEAK 3(2Q22.1) MUTATED 7 0
DEL PEAK 3(2Q22.1) WILD-TYPE 218 224

Figure S20.  Get High-res Image Gene #11: 'del_2q22.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_2q22.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.00482 (Fisher's exact test), Q value = 0.15

Table S21.  Gene #11: 'del_2q22.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients OTHER, SPECIFY THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED) THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
ALL 7 356 100 36
DEL PEAK 3(2Q22.1) MUTATED 0 3 7 0
DEL PEAK 3(2Q22.1) WILD-TYPE 7 353 93 36

Figure S21.  Get High-res Image Gene #11: 'del_2q22.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_2q22.1' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00663 (Wilcoxon-test), Q value = 0.18

Table S22.  Gene #11: 'del_2q22.1' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 386 3.6 (6.0)
DEL PEAK 3(2Q22.1) MUTATED 7 0.0 (0.0)
DEL PEAK 3(2Q22.1) WILD-TYPE 379 3.6 (6.0)

Figure S22.  Get High-res Image Gene #11: 'del_2q22.1' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'del_2q37.3' versus 'PATHOLOGIC_STAGE'

P value = 0.0128 (Fisher's exact test), Q value = 0.24

Table S23.  Gene #12: 'del_2q37.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
ALL 282 50 111 2 46 6
DEL PEAK 4(2Q37.3) MUTATED 4 6 2 0 1 0
DEL PEAK 4(2Q37.3) WILD-TYPE 278 44 109 2 45 6

Figure S23.  Get High-res Image Gene #12: 'del_2q37.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_2q37.3' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0155 (Wilcoxon-test), Q value = 0.25

Table S24.  Gene #12: 'del_2q37.3' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 386 3.6 (6.0)
DEL PEAK 4(2Q37.3) MUTATED 8 0.2 (0.7)
DEL PEAK 4(2Q37.3) WILD-TYPE 378 3.6 (6.0)

Figure S24.  Get High-res Image Gene #12: 'del_2q37.3' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'del_9p21.3' versus 'YEARS_TO_BIRTH'

P value = 0.00966 (Wilcoxon-test), Q value = 0.21

Table S25.  Gene #20: 'del_9p21.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 499 47.3 (15.8)
DEL PEAK 15(9P21.3) MUTATED 20 56.8 (16.0)
DEL PEAK 15(9P21.3) WILD-TYPE 479 46.9 (15.6)

Figure S25.  Get High-res Image Gene #20: 'del_9p21.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_9p21.3' versus 'PATHOLOGIC_STAGE'

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

Table S26.  Gene #20: 'del_9p21.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
ALL 282 50 111 2 46 6
DEL PEAK 15(9P21.3) MUTATED 7 5 4 2 1 1
DEL PEAK 15(9P21.3) WILD-TYPE 275 45 107 0 45 5

Figure S26.  Get High-res Image Gene #20: 'del_9p21.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_9q22.33' versus 'YEARS_TO_BIRTH'

P value = 0.000623 (Wilcoxon-test), Q value = 0.048

Table S27.  Gene #21: 'del_9q22.33' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 499 47.3 (15.8)
DEL PEAK 16(9Q22.33) MUTATED 27 59.2 (19.0)
DEL PEAK 16(9Q22.33) WILD-TYPE 472 46.6 (15.3)

Figure S27.  Get High-res Image Gene #21: 'del_9q22.33' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_9q22.33' versus 'PATHOLOGIC_STAGE'

P value = 0.00035 (Fisher's exact test), Q value = 0.036

Table S28.  Gene #21: 'del_9q22.33' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
ALL 282 50 111 2 46 6
DEL PEAK 16(9Q22.33) MUTATED 10 5 4 2 5 1
DEL PEAK 16(9Q22.33) WILD-TYPE 272 45 107 0 41 5

Figure S28.  Get High-res Image Gene #21: 'del_9q22.33' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_10q23.31' versus 'TUMOR_SIZE'

P value = 0.00234 (Wilcoxon-test), Q value = 0.11

Table S29.  Gene #24: 'del_10q23.31' versus Clinical Feature #15: 'TUMOR_SIZE'

nPatients Mean (Std.Dev)
ALL 401 3.0 (1.6)
DEL PEAK 19(10Q23.31) MUTATED 9 4.6 (1.5)
DEL PEAK 19(10Q23.31) WILD-TYPE 392 2.9 (1.6)

Figure S29.  Get High-res Image Gene #24: 'del_10q23.31' versus Clinical Feature #15: 'TUMOR_SIZE'

'del_13q12.3' versus 'YEARS_TO_BIRTH'

P value = 0.00132 (Wilcoxon-test), Q value = 0.081

Table S30.  Gene #25: 'del_13q12.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 499 47.3 (15.8)
DEL PEAK 20(13Q12.3) MUTATED 16 60.7 (15.5)
DEL PEAK 20(13Q12.3) WILD-TYPE 483 46.8 (15.6)

Figure S30.  Get High-res Image Gene #25: 'del_13q12.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_13q12.3' versus 'RADIATION_EXPOSURE'

P value = 0.00166 (Fisher's exact test), Q value = 0.092

Table S31.  Gene #25: 'del_13q12.3' versus Clinical Feature #10: 'RADIATION_EXPOSURE'

nPatients NO YES
ALL 420 17
DEL PEAK 20(13Q12.3) MUTATED 11 4
DEL PEAK 20(13Q12.3) WILD-TYPE 409 13

Figure S31.  Get High-res Image Gene #25: 'del_13q12.3' versus Clinical Feature #10: 'RADIATION_EXPOSURE'

'del_13q14.3' versus 'RADIATION_EXPOSURE'

P value = 0.00345 (Fisher's exact test), Q value = 0.11

Table S32.  Gene #26: 'del_13q14.3' versus Clinical Feature #10: 'RADIATION_EXPOSURE'

nPatients NO YES
ALL 420 17
DEL PEAK 21(13Q14.3) MUTATED 14 4
DEL PEAK 21(13Q14.3) WILD-TYPE 406 13

Figure S32.  Get High-res Image Gene #26: 'del_13q14.3' versus Clinical Feature #10: 'RADIATION_EXPOSURE'

'del_16q23.3' versus 'PATHOLOGIC_STAGE'

P value = 0.00215 (Fisher's exact test), Q value = 0.11

Table S33.  Gene #28: 'del_16q23.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
ALL 282 50 111 2 46 6
DEL PEAK 24(16Q23.3) MUTATED 0 0 3 0 2 1
DEL PEAK 24(16Q23.3) WILD-TYPE 282 50 108 2 44 5

Figure S33.  Get High-res Image Gene #28: 'del_16q23.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_17p13.1' versus 'TUMOR_SIZE'

P value = 0.0141 (Wilcoxon-test), Q value = 0.25

Table S34.  Gene #29: 'del_17p13.1' versus Clinical Feature #15: 'TUMOR_SIZE'

nPatients Mean (Std.Dev)
ALL 401 3.0 (1.6)
DEL PEAK 25(17P13.1) MUTATED 7 4.5 (1.6)
DEL PEAK 25(17P13.1) WILD-TYPE 394 2.9 (1.6)

Figure S34.  Get High-res Image Gene #29: 'del_17p13.1' versus Clinical Feature #15: 'TUMOR_SIZE'

'del_19p13.2' versus 'TUMOR_SIZE'

P value = 0.00278 (Wilcoxon-test), Q value = 0.11

Table S35.  Gene #31: 'del_19p13.2' versus Clinical Feature #15: 'TUMOR_SIZE'

nPatients Mean (Std.Dev)
ALL 401 3.0 (1.6)
DEL PEAK 27(19P13.2) MUTATED 4 5.8 (0.6)
DEL PEAK 27(19P13.2) WILD-TYPE 397 2.9 (1.6)

Figure S35.  Get High-res Image Gene #31: 'del_19p13.2' versus Clinical Feature #15: 'TUMOR_SIZE'

'del_19p13.12' versus 'TUMOR_SIZE'

P value = 0.00769 (Wilcoxon-test), Q value = 0.19

Table S36.  Gene #32: 'del_19p13.12' versus Clinical Feature #15: 'TUMOR_SIZE'

nPatients Mean (Std.Dev)
ALL 401 3.0 (1.6)
DEL PEAK 28(19P13.12) MUTATED 5 5.2 (1.6)
DEL PEAK 28(19P13.12) WILD-TYPE 396 2.9 (1.6)

Figure S36.  Get High-res Image Gene #32: 'del_19p13.12' versus Clinical Feature #15: 'TUMOR_SIZE'

'del_21q21.1' versus 'PATHOLOGIC_STAGE'

P value = 0.00669 (Fisher's exact test), Q value = 0.18

Table S37.  Gene #33: 'del_21q21.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
ALL 282 50 111 2 46 6
DEL PEAK 30(21Q21.1) MUTATED 1 4 2 0 2 0
DEL PEAK 30(21Q21.1) WILD-TYPE 281 46 109 2 44 6

Figure S37.  Get High-res Image Gene #33: 'del_21q21.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_xq28' versus 'PATHOLOGIC_STAGE'

P value = 0.00098 (Fisher's exact test), Q value = 0.067

Table S38.  Gene #36: 'del_xq28' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
ALL 282 50 111 2 46 6
DEL PEAK 33(XQ28) MUTATED 0 4 0 0 0 0
DEL PEAK 33(XQ28) WILD-TYPE 282 46 111 2 46 6

Figure S38.  Get High-res Image Gene #36: 'del_xq28' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

Methods & Data
Input

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

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/THCA-TP/22511444/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/THCA-TP/22507188/THCA-TP.merged_data.txt

  • Number of patients = 499

  • Number of significantly focal cnvs = 36

  • 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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