Correlation between copy number variations of arm-level result and selected clinical features
Thyroid Adenocarcinoma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C1571B4B
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1571B4B
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 59 arm-level events and 17 clinical features across 499 patients, 131 significant findings detected with Q value < 0.25.

  • 1p gain cnv correlated to 'Time to Death',  'NEOPLASM_DISEASESTAGE', and 'PATHOLOGY_T_STAGE'.

  • 1q gain cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'HISTOLOGICAL_TYPE',  'EXTRATHYROIDAL_EXTENSION',  'COMPLETENESS_OF_RESECTION',  'MULTIFOCALITY',  'TUMOR_SIZE', and 'RACE'.

  • 3p gain cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'PATHOLOGY_M_STAGE', and 'COMPLETENESS_OF_RESECTION'.

  • 4p gain cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'PATHOLOGY_N_STAGE', and 'NUMBER_OF_LYMPH_NODES'.

  • 4q gain cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'PATHOLOGY_N_STAGE', and 'NUMBER_OF_LYMPH_NODES'.

  • 5p gain cnv correlated to 'YEARS_TO_BIRTH',  'NEOPLASM_DISEASESTAGE',  'EXTRATHYROIDAL_EXTENSION', and 'TUMOR_SIZE'.

  • 5q gain cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_N_STAGE',  'EXTRATHYROIDAL_EXTENSION', and 'NUMBER_OF_LYMPH_NODES'.

  • 7p gain cnv correlated to 'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_N_STAGE',  'HISTOLOGICAL_TYPE',  'EXTRATHYROIDAL_EXTENSION', and 'NUMBER_OF_LYMPH_NODES'.

  • 7q gain cnv correlated to 'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_N_STAGE',  'HISTOLOGICAL_TYPE',  'EXTRATHYROIDAL_EXTENSION', and 'NUMBER_OF_LYMPH_NODES'.

  • 8q gain cnv correlated to 'EXTRATHYROIDAL_EXTENSION'.

  • 9q gain cnv correlated to 'YEARS_TO_BIRTH' and 'TUMOR_SIZE'.

  • 12p gain cnv correlated to 'PATHOLOGY_N_STAGE',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • 12q gain cnv correlated to 'PATHOLOGY_N_STAGE',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • 14q gain cnv correlated to 'NEOPLASM_DISEASESTAGE'.

  • 16p gain cnv correlated to 'PATHOLOGY_N_STAGE',  'EXTRATHYROIDAL_EXTENSION', and 'NUMBER_OF_LYMPH_NODES'.

  • 16q gain cnv correlated to 'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_N_STAGE',  'EXTRATHYROIDAL_EXTENSION', and 'NUMBER_OF_LYMPH_NODES'.

  • 17p gain cnv correlated to 'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_N_STAGE', and 'NUMBER_OF_LYMPH_NODES'.

  • 17q gain cnv correlated to 'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_N_STAGE', and 'NUMBER_OF_LYMPH_NODES'.

  • 18p gain cnv correlated to 'PATHOLOGY_N_STAGE'.

  • 18q gain cnv correlated to 'PATHOLOGY_N_STAGE'.

  • 19p gain cnv correlated to 'PATHOLOGY_N_STAGE',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • 19q gain cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGY_N_STAGE',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • 20p gain cnv correlated to 'NEOPLASM_DISEASESTAGE',  'HISTOLOGICAL_TYPE',  'EXTRATHYROIDAL_EXTENSION', and 'NUMBER_OF_LYMPH_NODES'.

  • 20q gain cnv correlated to 'NEOPLASM_DISEASESTAGE',  'HISTOLOGICAL_TYPE',  'EXTRATHYROIDAL_EXTENSION', and 'NUMBER_OF_LYMPH_NODES'.

  • xp gain cnv correlated to 'YEARS_TO_BIRTH',  'NEOPLASM_DISEASESTAGE',  'EXTRATHYROIDAL_EXTENSION', and 'NUMBER_OF_LYMPH_NODES'.

  • xq gain cnv correlated to 'NEOPLASM_DISEASESTAGE' and 'EXTRATHYROIDAL_EXTENSION'.

  • 2p loss cnv correlated to 'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_N_STAGE',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • 2q loss cnv correlated to 'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_N_STAGE',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • 6q loss cnv correlated to 'Time to Death' and 'TUMOR_SIZE'.

  • 9p loss cnv correlated to 'NEOPLASM_DISEASESTAGE'.

  • 9q loss cnv correlated to 'YEARS_TO_BIRTH' and 'NEOPLASM_DISEASESTAGE'.

  • 10p loss cnv correlated to 'PATHOLOGY_N_STAGE',  'NUMBER_OF_LYMPH_NODES', and 'TUMOR_SIZE'.

  • 10q loss cnv correlated to 'PATHOLOGY_N_STAGE' and 'TUMOR_SIZE'.

  • 11p loss cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'NEOPLASM_DISEASESTAGE',  'GENDER', and 'TUMOR_SIZE'.

  • 11q loss cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'NEOPLASM_DISEASESTAGE',  'GENDER', and 'TUMOR_SIZE'.

  • 13q loss cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGY_N_STAGE',  'RADIATION_EXPOSURE', and 'NUMBER_OF_LYMPH_NODES'.

  • 17p loss cnv correlated to 'RADIATIONS_RADIATION_REGIMENINDICATION' and 'TUMOR_SIZE'.

  • 19p loss cnv correlated to 'RADIATION_EXPOSURE' and 'TUMOR_SIZE'.

  • 21q loss cnv correlated to 'NEOPLASM_DISEASESTAGE'.

  • xp loss cnv correlated to 'NEOPLASM_DISEASESTAGE'.

  • xq loss cnv correlated to 'NEOPLASM_DISEASESTAGE'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 59 arm-level events and 17 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 131 significant findings detected.

Clinical
Features 		Time
to
Death 		YEARS
TO
BIRTH 		NEOPLASM
DISEASESTAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER HISTOLOGICAL
TYPE 		RADIATIONS
RADIATION
REGIMENINDICATION 		RADIATION
EXPOSURE 		EXTRATHYROIDAL
EXTENSION 		COMPLETENESS
OF
RESECTION 		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
1q gain 26 (5%) 473 0.014
(0.171) 		1.76e-05
(0.00589) 		1e-05
(0.00501) 		1e-05
(0.00501) 		0.000657
(0.0607) 		0.368
(0.994) 		0.65
(1.00) 		0.0183
(0.192) 		0.532
(1.00) 		1
(1.00) 		0.00013
(0.0325) 		0.0266
(0.236) 		0.0607
(0.371) 		0.0244
(0.222) 		0.00401
(0.119) 		0.0025
(0.109) 		0.271
(0.859)
5q gain 17 (3%) 482 0.023
(0.214) 		0.0075
(0.134) 		0.00969
(0.154) 		0.351
(0.964) 		0.0116
(0.164) 		1
(1.00) 		0.41
(1.00) 		0.0616
(0.371) 		0.388
(1.00) 		1
(1.00) 		0.0173
(0.188) 		0.393
(1.00) 		0.00348
(0.119) 		1
(1.00) 		0.0756
(0.424) 		0.557
(1.00) 		0.608
(1.00)
7p gain 18 (4%) 481 0.437
(1.00) 		0.0443
(0.3) 		0.0102
(0.156) 		0.418
(1.00) 		0.00649
(0.134) 		1
(1.00) 		1
(1.00) 		0.0231
(0.214) 		1
(1.00) 		1
(1.00) 		0.00526
(0.13) 		0.393
(1.00) 		0.00196
(0.0982) 		1
(1.00) 		0.367
(0.994) 		0.56
(1.00) 		0.608
(1.00)
7q gain 20 (4%) 479 0.487
(1.00) 		0.0371
(0.266) 		0.0179
(0.189) 		0.565
(1.00) 		0.00649
(0.134) 		1
(1.00) 		1
(1.00) 		0.014
(0.171) 		1
(1.00) 		1
(1.00) 		0.0188
(0.192) 		0.218
(0.757) 		0.00196
(0.0982) 		1
(1.00) 		0.383
(1.00) 		0.488
(1.00) 		0.608
(1.00)
11p loss 7 (1%) 492 0.00266
(0.111) 		0.000665
(0.0607) 		0.00544
(0.13) 		0.235
(0.785) 		0.285
(0.877) 		1
(1.00) 		0.0164
(0.181) 		0.819
(1.00) 		0.182
(0.684) 		1
(1.00) 		0.559
(1.00) 		0.529
(1.00) 		0.208
(0.737) 		0.708
(1.00) 		0.00797
(0.138) 		0.476
(1.00) 		1
(1.00)
11q loss 9 (2%) 490 0.0054
(0.13) 		0.000199
(0.0332) 		0.00357
(0.119) 		0.234
(0.785) 		0.338
(0.94) 		1
(1.00) 		0.00184
(0.0982) 		1
(1.00) 		0.228
(0.776) 		1
(1.00) 		0.806
(1.00) 		0.519
(1.00) 		0.313
(0.927) 		1
(1.00) 		0.00239
(0.109) 		0.548
(1.00) 		1
(1.00)
3p gain 3 (1%) 496 0.00388
(0.119) 		0.0153
(0.176) 		0.034
(0.256) 		0.0957
(0.471) 		1
(1.00) 		0.0315
(0.247) 		0.568
(1.00) 		0.227
(0.776) 		1
(1.00) 		1
(1.00) 		0.61
(1.00) 		0.0233
(0.214) 		1
(1.00) 		0.547
(1.00) 		1
(1.00)
4p gain 5 (1%) 494 0.011
(0.157) 		0.0295
(0.246) 		0.183
(0.684) 		0.708
(1.00) 		0.0302
(0.246) 		1
(1.00) 		0.181
(0.684) 		0.133
(0.576) 		1
(1.00) 		1
(1.00) 		0.393
(1.00) 		0.0228
(0.214) 		0.185
(0.686) 		0.245
(0.803) 		1
(1.00) 		1
(1.00)
4q gain 5 (1%) 494 0.011
(0.157) 		0.0295
(0.246) 		0.183
(0.684) 		0.709
(1.00) 		0.0302
(0.246) 		1
(1.00) 		0.179
(0.684) 		0.133
(0.576) 		1
(1.00) 		1
(1.00) 		0.391
(1.00) 		0.0228
(0.214) 		0.185
(0.686) 		0.245
(0.803) 		1
(1.00) 		1
(1.00)
5p gain 21 (4%) 478 0.0905
(0.459) 		0.000162
(0.0325) 		0.00396
(0.119) 		0.268
(0.855) 		0.228
(0.776) 		1
(1.00) 		0.458
(1.00) 		0.159
(0.648) 		0.457
(1.00) 		1
(1.00) 		0.0207
(0.204) 		0.399
(1.00) 		0.0705
(0.4) 		0.509
(1.00) 		0.0296
(0.246) 		0.298
(0.907) 		1
(1.00)
16q gain 13 (3%) 486 0.192
(0.706) 		0.131
(0.575) 		0.0218
(0.212) 		0.745
(1.00) 		0.0201
(0.202) 		1
(1.00) 		1
(1.00) 		0.0443
(0.3) 		1
(1.00) 		1
(1.00) 		0.0137
(0.171) 		0.275
(0.861) 		0.00383
(0.119) 		1
(1.00) 		0.631
(1.00) 		0.779
(1.00) 		1
(1.00)
19q gain 10 (2%) 489 0.0629
(0.371) 		0.0158
(0.178) 		0.605
(1.00) 		0.333
(0.935) 		0.00733
(0.134) 		0.14
(0.596) 		0.00463
(0.126) 		0.25
(0.808) 		1
(1.00) 		0.529
(1.00) 		0.823
(1.00) 		0.00691
(0.134) 		0.524
(1.00) 		0.0837
(0.433) 		1
(1.00) 		1
(1.00)
20p gain 12 (2%) 487 0.316
(0.927) 		0.0824
(0.428) 		0.00982
(0.154) 		0.578
(1.00) 		0.0372
(0.266) 		0.529
(1.00) 		0.00401
(0.119) 		1
(1.00) 		1
(1.00) 		0.014
(0.171) 		0.857
(1.00) 		0.00691
(0.134) 		0.779
(1.00) 		0.0969
(0.472) 		1
(1.00) 		1
(1.00)
20q gain 12 (2%) 487 0.316
(0.927) 		0.0824
(0.428) 		0.0103
(0.156) 		0.578
(1.00) 		0.0372
(0.266) 		0.529
(1.00) 		0.00421
(0.119) 		1
(1.00) 		1
(1.00) 		0.0136
(0.171) 		0.859
(1.00) 		0.00691
(0.134) 		0.779
(1.00) 		0.0969
(0.472) 		1
(1.00) 		1
(1.00)
xp gain 8 (2%) 491 0.0803
(0.424) 		0.0138
(0.171) 		0.0081
(0.138) 		0.323
(0.935) 		0.0679
(0.387) 		1
(1.00) 		0.688
(1.00) 		0.217
(0.757) 		1
(1.00) 		0.273
(0.86) 		0.0177
(0.189) 		0.0633
(0.371) 		0.0125
(0.17) 		0.48
(1.00) 		0.47
(1.00) 		1
(1.00) 		1
(1.00)
2p loss 10 (2%) 489 0.699
(1.00) 		0.283
(0.877) 		0.0307
(0.246) 		0.677
(1.00) 		0.0036
(0.119) 		1
(1.00) 		0.731
(1.00) 		0.00485
(0.128) 		1
(1.00) 		1
(1.00) 		0.15
(0.625) 		0.456
(1.00) 		0.00383
(0.119) 		1
(1.00) 		0.977
(1.00) 		1
(1.00) 		1
(1.00)
2q loss 10 (2%) 489 0.587
(1.00) 		0.257
(0.821) 		0.0307
(0.246) 		0.793
(1.00) 		0.00733
(0.134) 		1
(1.00) 		0.731
(1.00) 		0.00517
(0.13) 		1
(1.00) 		1
(1.00) 		0.151
(0.625) 		0.456
(1.00) 		0.00691
(0.134) 		1
(1.00) 		0.364
(0.993) 		1
(1.00) 		1
(1.00)
13q loss 14 (3%) 485 0.306
(0.917) 		0.0299
(0.246) 		0.285
(0.877) 		0.918
(1.00) 		0.00572
(0.133) 		1
(1.00) 		0.539
(1.00) 		0.46
(1.00) 		0.332
(0.935) 		0.000641
(0.0607) 		0.499
(1.00) 		0.679
(1.00) 		0.0161
(0.179) 		0.792
(1.00) 		0.0982
(0.472) 		0.712
(1.00) 		0.615
(1.00)
1p gain 5 (1%) 494 0.00415
(0.119) 		0.0677
(0.387) 		0.0006
(0.0607) 		0.0315
(0.247) 		0.372
(0.996) 		0.0621
(0.371) 		1
(1.00) 		0.317
(0.928) 		1
(1.00) 		0.147
(0.617) 		0.202
(0.724) 		0.103
(0.492) 		0.623
(1.00) 		0.38
(1.00) 		0.254
(0.816) 		0.402
(1.00) 		1
(1.00)
12p gain 14 (3%) 485 0.525
(1.00) 		0.204
(0.726) 		0.0953
(0.471) 		0.896
(1.00) 		0.000862
(0.0617) 		1
(1.00) 		0.769
(1.00) 		0.0155
(0.177) 		1
(1.00) 		1
(1.00) 		0.203
(0.724) 		0.462
(1.00) 		0.00119
(0.0744) 		0.792
(1.00) 		0.963
(1.00) 		0.778
(1.00) 		1
(1.00)
12q gain 15 (3%) 484 0.523
(1.00) 		0.178
(0.684) 		0.132
(0.575) 		0.883
(1.00) 		0.000862
(0.0617) 		1
(1.00) 		0.769
(1.00) 		0.00615
(0.134) 		1
(1.00) 		1
(1.00) 		0.176
(0.684) 		0.607
(1.00) 		0.00119
(0.0744) 		1
(1.00) 		0.963
(1.00) 		0.666
(1.00) 		1
(1.00)
16p gain 15 (3%) 484 0.239
(0.793) 		0.198
(0.718) 		0.0381
(0.271) 		0.925
(1.00) 		0.0108
(0.157) 		1
(1.00) 		0.769
(1.00) 		0.0958
(0.471) 		1
(1.00) 		1
(1.00) 		0.0255
(0.231) 		0.142
(0.598) 		0.00213
(0.102) 		0.794
(1.00) 		0.695
(1.00) 		0.558
(1.00) 		1
(1.00)
17p gain 16 (3%) 483 0.406
(1.00) 		0.0805
(0.424) 		0.00427
(0.119) 		0.857
(1.00) 		0.0206
(0.204) 		1
(1.00) 		1
(1.00) 		0.0371
(0.266) 		1
(1.00) 		1
(1.00) 		0.779
(1.00) 		0.328
(0.935) 		0.0177
(0.189) 		1
(1.00) 		0.527
(1.00) 		1
(1.00) 		0.608
(1.00)
17q gain 18 (4%) 481 0.393
(1.00) 		0.103
(0.492) 		0.0106
(0.157) 		0.497
(1.00) 		0.0322
(0.249) 		1
(1.00) 		1
(1.00) 		0.0858
(0.439) 		1
(1.00) 		1
(1.00) 		0.408
(1.00) 		0.567
(1.00) 		0.0321
(0.249) 		0.634
(1.00) 		0.576
(1.00) 		1
(1.00) 		0.61
(1.00)
19p gain 8 (2%) 491 0.693
(1.00) 		0.0527
(0.35) 		0.626
(1.00) 		0.622
(1.00) 		0.0149
(0.174) 		0.218
(0.757) 		0.0079
(0.138) 		1
(1.00) 		1
(1.00) 		0.603
(1.00) 		0.469
(1.00) 		0.0125
(0.17) 		0.151
(0.625) 		0.155
(0.634) 		1
(1.00) 		1
(1.00)
10p loss 7 (1%) 492 0.623
(1.00) 		0.33
(0.935) 		0.124
(0.546) 		0.284
(0.877) 		0.0149
(0.174) 		1
(1.00) 		0.39
(1.00) 		0.389
(1.00) 		1
(1.00) 		1
(1.00) 		0.755
(1.00) 		1
(1.00) 		0.0228
(0.214) 		0.708
(1.00) 		0.0119
(0.165) 		0.673
(1.00) 		1
(1.00)
9q gain 4 (1%) 495 0.687
(1.00) 		0.0325
(0.249) 		0.0406
(0.287) 		0.634
(1.00) 		0.372
(0.996) 		1
(1.00) 		0.29
(0.885) 		0.454
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.241
(0.796) 		0.338
(0.94) 		0.0265
(0.236) 		1
(1.00) 		1
(1.00)
xq gain 9 (2%) 490 0.0893
(0.455) 		0.0571
(0.369) 		0.0146
(0.174) 		0.475
(1.00) 		0.175
(0.684) 		1
(1.00) 		0.456
(1.00) 		0.335
(0.935) 		1
(1.00) 		0.302
(0.914) 		0.0189
(0.192) 		0.0846
(0.435) 		0.093
(0.464) 		0.313
(0.927) 		0.47
(1.00) 		1
(1.00) 		1
(1.00)
6q loss 7 (1%) 492 0.00192
(0.0982) 		0.08
(0.424) 		0.201
(0.724) 		0.795
(1.00) 		0.216
(0.757) 		0.39
(1.00) 		0.818
(1.00) 		0.182
(0.684) 		0.213
(0.751) 		0.396
(1.00) 		0.762
(1.00) 		0.177
(0.684) 		0.46
(1.00) 		0.00963
(0.154) 		1
(1.00) 		1
(1.00)
9q loss 25 (5%) 474 0.0346
(0.259) 		0.000793
(0.0617) 		0.00042
(0.0602) 		0.0982
(0.472) 		0.656
(1.00) 		0.277
(0.867) 		0.352
(0.964) 		1
(1.00) 		0.518
(1.00) 		1
(1.00) 		0.0632
(0.371) 		0.806
(1.00) 		0.709
(1.00) 		0.681
(1.00) 		0.0575
(0.37) 		0.503
(1.00) 		1
(1.00)
10q loss 6 (1%) 493 0.676
(1.00) 		0.307
(0.917) 		0.256
(0.819) 		0.331
(0.935) 		0.0302
(0.246) 		1
(1.00) 		0.195
(0.71) 		0.78
(1.00) 		1
(1.00) 		1
(1.00) 		0.749
(1.00) 		1
(1.00) 		0.0421
(0.289) 		0.421
(1.00) 		0.00858
(0.143) 		0.669
(1.00) 		1
(1.00)
17p loss 8 (2%) 491 0.559
(1.00) 		0.885
(1.00) 		0.155
(0.634) 		0.034
(0.256) 		0.503
(1.00) 		1
(1.00) 		1
(1.00) 		0.217
(0.757) 		0.0186
(0.192) 		0.273
(0.86) 		0.062
(0.371) 		0.345
(0.951) 		0.898
(1.00) 		0.731
(1.00) 		0.0149
(0.174) 		0.586
(1.00) 		1
(1.00)
19p loss 5 (1%) 494 0.142
(0.598) 		0.492
(1.00) 		0.253
(0.816) 		1
(1.00) 		0.623
(1.00) 		1
(1.00) 		0.613
(1.00) 		1
(1.00) 		1
(1.00) 		0.0133
(0.171) 		1
(1.00) 		0.644
(1.00) 		0.38
(1.00) 		0.00941
(0.154) 		1
(1.00) 		1
(1.00)
8q gain 7 (1%) 492 0.0808
(0.424) 		0.345
(0.951) 		0.0557
(0.363) 		0.398
(1.00) 		0.685
(1.00) 		1
(1.00) 		0.681
(1.00) 		0.818
(1.00) 		1
(1.00) 		1
(1.00) 		0.00739
(0.134) 		0.397
(1.00) 		0.177
(0.684) 		0.131
(0.575) 		0.23
(0.777) 		0.733
(1.00) 		1
(1.00)
14q gain 11 (2%) 488 0.539
(1.00) 		0.0365
(0.266) 		0.00703
(0.134) 		0.377
(1.00) 		0.0372
(0.266) 		1
(1.00) 		0.303
(0.914) 		0.055
(0.363) 		1
(1.00) 		1
(1.00) 		0.831
(1.00) 		0.498
(1.00) 		0.0556
(0.363) 		0.123
(0.546) 		0.274
(0.86) 		0.762
(1.00) 		1
(1.00)
18p gain 6 (1%) 493 0.607
(1.00) 		0.715
(1.00) 		0.713
(1.00) 		0.763
(1.00) 		0.0302
(0.246) 		1
(1.00) 		0.66
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.393
(1.00) 		0.0421
(0.289) 		0.692
(1.00) 		0.813
(1.00) 		1
(1.00) 		1
(1.00)
18q gain 6 (1%) 493 0.607
(1.00) 		0.715
(1.00) 		0.714
(1.00) 		0.765
(1.00) 		0.0302
(0.246) 		1
(1.00) 		0.66
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.392
(1.00) 		0.0421
(0.289) 		0.692
(1.00) 		0.813
(1.00) 		1
(1.00) 		1
(1.00)
9p loss 19 (4%) 480 0.447
(1.00) 		0.0931
(0.464) 		0.0274
(0.241) 		0.494
(1.00) 		1
(1.00) 		0.202
(0.724) 		0.299
(0.91) 		0.729
(1.00) 		1
(1.00) 		1
(1.00) 		0.898
(1.00) 		0.564
(1.00) 		0.32
(0.933) 		0.486
(1.00) 		0.12
(0.546) 		1
(1.00) 		0.379
(1.00)
21q loss 8 (2%) 491 0.783
(1.00) 		0.117
(0.546) 		0.0135
(0.171) 		0.175
(0.684) 		0.503
(1.00) 		1
(1.00) 		0.445
(1.00) 		0.852
(1.00) 		1
(1.00) 		1
(1.00) 		0.177
(0.684) 		1
(1.00) 		0.598
(1.00) 		0.151
(0.625) 		0.516
(1.00) 		0.236
(0.788) 		1
(1.00)
xp loss 4 (1%) 495 0.768
(1.00) 		0.947
(1.00) 		0.0316
(0.247) 		0.308
(0.918) 		0.372
(0.996) 		0.29
(0.885) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.648
(1.00) 		1
(1.00) 		0.492
(1.00) 		1
(1.00) 		1
(1.00)
xq loss 3 (1%) 496 0.779
(1.00) 		0.424
(1.00) 		0.00597
(0.134) 		0.19
(0.701) 		0.123
(0.546) 		0.175
(0.684) 		0.637
(1.00) 		1
(1.00) 		1
(1.00) 		0.613
(1.00) 		1
(1.00) 		0.0788
(0.424) 		1
(1.00) 		1
(1.00)
8p gain 6 (1%) 493 0.647
(1.00) 		0.648
(1.00) 		0.713
(1.00) 		0.834
(1.00) 		0.372
(0.996) 		1
(1.00) 		1
(1.00) 		0.783
(1.00) 		1
(1.00) 		1
(1.00) 		0.366
(0.994) 		0.466
(1.00) 		0.177
(0.684) 		0.225
(0.775) 		0.344
(0.951) 		0.67
(1.00) 		1
(1.00)
9p gain 3 (1%) 496 0.721
(1.00) 		0.0792
(0.424) 		0.0473
(0.318) 		0.693
(1.00) 		0.123
(0.546) 		1
(1.00) 		1
(1.00) 		0.226
(0.776) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.597
(1.00) 		0.0623
(0.371) 		1
(1.00)
11p gain 6 (1%) 493 0.546
(1.00) 		0.764
(1.00) 		0.712
(1.00) 		0.766
(1.00) 		0.0611
(0.371) 		1
(1.00) 		0.195
(0.71) 		0.247
(0.806) 		1
(1.00) 		1
(1.00) 		0.364
(0.993) 		0.462
(1.00) 		0.0788
(0.424) 		0.225
(0.775) 		0.63
(1.00) 		1
(1.00) 		1
(1.00)
11q gain 5 (1%) 494 0.548
(1.00) 		0.752
(1.00) 		0.8
(1.00) 		0.893
(1.00) 		0.123
(0.546) 		1
(1.00) 		0.613
(1.00) 		0.561
(1.00) 		1
(1.00) 		1
(1.00) 		0.452
(1.00) 		0.392
(1.00) 		0.0652
(0.378) 		0.96
(1.00) 		1
(1.00) 		1
(1.00)
13q gain 5 (1%) 494 0.732
(1.00) 		0.152
(0.626) 		0.0583
(0.371) 		0.639
(1.00) 		0.0611
(0.371) 		1
(1.00) 		1
(1.00) 		0.183
(0.684) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.0421
(0.289) 		0.665
(1.00) 		0.688
(1.00) 		1
(1.00)
21q gain 5 (1%) 494 0.613
(1.00) 		0.324
(0.935) 		0.583
(1.00) 		0.566
(1.00) 		0.123
(0.546) 		1
(1.00) 		0.613
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.647
(1.00) 		0.315
(0.927) 		0.0652
(0.378) 		0.122
(0.546) 		1
(1.00) 		1
(1.00)
1p loss 4 (1%) 495 0.639
(1.00) 		0.542
(1.00) 		0.138
(0.587) 		0.631
(1.00) 		0.123
(0.546) 		1
(1.00) 		0.578
(1.00) 		0.458
(1.00) 		1
(1.00) 		1
(1.00) 		0.643
(1.00) 		1
(1.00) 		0.628
(1.00) 		0.12
(0.546) 		0.488
(1.00) 		1
(1.00)
1q loss 3 (1%) 496 0.642
(1.00) 		0.816
(1.00) 		0.335
(0.935) 		0.807
(1.00) 		0.248
(0.806) 		0.568
(1.00) 		0.23
(0.777) 		1
(1.00) 		1
(1.00) 		0.611
(1.00) 		1
(1.00) 		1
(1.00) 		0.12
(0.546) 		1
(1.00)
3p loss 3 (1%) 496 0.692
(1.00) 		0.568
(1.00) 		0.332
(0.935) 		0.809
(1.00) 		0.248
(0.806) 		1
(1.00) 		0.637
(1.00) 		1
(1.00) 		1
(1.00) 		0.611
(1.00) 		1
(1.00) 		0.597
(1.00) 		0.0808
(0.424) 		1
(1.00) 		1
(1.00)
3q loss 4 (1%) 495 0.636
(1.00) 		0.595
(1.00) 		0.137
(0.587) 		0.632
(1.00) 		0.123
(0.546) 		1
(1.00) 		0.458
(1.00) 		1
(1.00) 		1
(1.00) 		0.646
(1.00) 		1
(1.00) 		0.0788
(0.424) 		1
(1.00) 		0.0983
(0.472) 		1
(1.00) 		1
(1.00)
6p loss 4 (1%) 495 0.669
(1.00) 		0.321
(0.933) 		0.734
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.645
(1.00) 		0.557
(1.00) 		1
(1.00) 		0.0596
(0.371) 		1
(1.00) 		1
(1.00)
8p loss 4 (1%) 495 0.821
(1.00) 		0.902
(1.00) 		0.176
(0.684) 		0.872
(1.00) 		0.123
(0.546) 		1
(1.00) 		0.0598
(0.371) 		0.457
(1.00) 		1
(1.00) 		1
(1.00) 		0.644
(1.00) 		1
(1.00) 		0.0788
(0.424) 		1
(1.00) 		0.75
(1.00) 		1
(1.00)
8q loss 4 (1%) 495 0.821
(1.00) 		0.902
(1.00) 		0.176
(0.684) 		0.87
(1.00) 		0.123
(0.546) 		1
(1.00) 		0.0598
(0.371) 		0.456
(1.00) 		1
(1.00) 		1
(1.00) 		0.645
(1.00) 		1
(1.00) 		0.0788
(0.424) 		1
(1.00) 		0.75
(1.00) 		1
(1.00)
15q loss 8 (2%) 491 0.547
(1.00) 		0.765
(1.00) 		0.243
(0.801) 		0.729
(1.00) 		0.0679
(0.387) 		0.0918
(0.463) 		0.688
(1.00) 		0.0505
(0.338) 		1
(1.00) 		1
(1.00) 		0.602
(1.00) 		0.786
(1.00) 		0.136
(0.587) 		0.731
(1.00) 		0.0794
(0.424) 		0.669
(1.00) 		0.398
(1.00)
17q loss 4 (1%) 495 0.827
(1.00) 		0.471
(1.00) 		0.473
(1.00) 		0.634
(1.00) 		0.0611
(0.371) 		1
(1.00) 		1
(1.00) 		0.454
(1.00) 		0.108
(0.51) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.0788
(0.424) 		1
(1.00) 		0.406
(1.00) 		1
(1.00)
18p loss 4 (1%) 495 0.746
(1.00) 		0.682
(1.00) 		0.177
(0.684) 		0.307
(0.917) 		0.623
(1.00) 		1
(1.00) 		1
(1.00) 		0.454
(1.00) 		1
(1.00) 		1
(1.00) 		0.643
(1.00) 		1
(1.00) 		0.332
(0.935) 		0.628
(1.00) 		0.635
(1.00) 		0.183
(0.684)
18q loss 4 (1%) 495 0.746
(1.00) 		0.682
(1.00) 		0.176
(0.684) 		0.306
(0.917) 		0.623
(1.00) 		1
(1.00) 		1
(1.00) 		0.458
(1.00) 		1
(1.00) 		1
(1.00) 		0.642
(1.00) 		1
(1.00) 		0.332
(0.935) 		0.628
(1.00) 		0.635
(1.00) 		0.183
(0.684)
22q loss 88 (18%) 411 0.397
(1.00) 		0.498
(1.00) 		0.679
(1.00) 		0.696
(1.00) 		0.326
(0.935) 		0.641
(1.00) 		0.508
(1.00) 		0.195
(0.71) 		0.481
(1.00) 		0.332
(0.935) 		0.432
(1.00) 		0.28
(0.873) 		0.49
(1.00) 		0.233
(0.785) 		0.491
(1.00) 		0.4
(1.00) 		1
(1.00)
'1p gain' versus 'Time to Death'

P value = 0.00415 (logrank test), Q value = 0.12

Table S1.  Gene #1: '1p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 497 14 0.1 - 169.3 (20.4)
1P GAIN MUTATED 5 1 1.0 - 57.6 (4.2)
1P GAIN WILD-TYPE 492 13 0.1 - 169.3 (20.4)

Figure S1.  Get High-res Image Gene #1: '1p gain' versus Clinical Feature #1: 'Time to Death'

'1p gain' versus 'NEOPLASM_DISEASESTAGE'

P value = 6e-04 (Fisher's exact test), Q value = 0.061

Table S2.  Gene #1: '1p gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
ALL 282 52 109 2 46 6
1P GAIN MUTATED 0 0 1 0 3 1
1P GAIN WILD-TYPE 282 52 108 2 43 5

Figure S2.  Get High-res Image Gene #1: '1p gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'1p gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.0315 (Fisher's exact test), Q value = 0.25

Table S3.  Gene #1: '1p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 141 166 167 23
1P GAIN MUTATED 1 1 1 2
1P GAIN WILD-TYPE 140 165 166 21

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

'1q gain' versus 'Time to Death'

P value = 0.014 (logrank test), Q value = 0.17

Table S4.  Gene #2: '1q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 497 14 0.1 - 169.3 (20.4)
1Q GAIN MUTATED 25 3 1.0 - 136.0 (27.2)
1Q GAIN WILD-TYPE 472 11 0.1 - 169.3 (20.1)

Figure S4.  Get High-res Image Gene #2: '1q gain' versus Clinical Feature #1: 'Time to Death'

'1q gain' versus 'YEARS_TO_BIRTH'

P value = 1.76e-05 (Wilcoxon-test), Q value = 0.0059

Table S5.  Gene #2: '1q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 499 47.2 (15.8)
1Q GAIN MUTATED 26 61.0 (15.3)
1Q GAIN WILD-TYPE 473 46.4 (15.5)

Figure S5.  Get High-res Image Gene #2: '1q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'1q gain' versus 'NEOPLASM_DISEASESTAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S6.  Gene #2: '1q gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
ALL 282 52 109 2 46 6
1Q GAIN MUTATED 6 0 10 1 8 1
1Q GAIN WILD-TYPE 276 52 99 1 38 5

Figure S6.  Get High-res Image Gene #2: '1q gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'1q gain' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.005

Table S7.  Gene #2: '1q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 141 166 167 23
1Q GAIN MUTATED 2 3 15 6
1Q GAIN WILD-TYPE 139 163 152 17

Figure S7.  Get High-res Image Gene #2: '1q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'1q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.000657 (Fisher's exact test), Q value = 0.061

Table S8.  Gene #2: '1q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 224 225
1Q GAIN MUTATED 4 21
1Q GAIN WILD-TYPE 220 204

Figure S8.  Get High-res Image Gene #2: '1q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'1q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0183 (Fisher's exact test), Q value = 0.19

Table S9.  Gene #2: '1q gain' versus Clinical Feature #8: '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 9 356 98 36
1Q GAIN MUTATED 0 23 0 3
1Q GAIN WILD-TYPE 9 333 98 33

Figure S9.  Get High-res Image Gene #2: '1q gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'1q gain' versus 'EXTRATHYROIDAL_EXTENSION'

P value = 0.00013 (Fisher's exact test), Q value = 0.032

Table S10.  Gene #2: '1q gain' versus Clinical Feature #11: 'EXTRATHYROIDAL_EXTENSION'

nPatients MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE VERY ADVANCED (T4B)
ALL 132 18 330 1
1Q GAIN MUTATED 11 4 10 1
1Q GAIN WILD-TYPE 121 14 320 0

Figure S10.  Get High-res Image Gene #2: '1q gain' versus Clinical Feature #11: 'EXTRATHYROIDAL_EXTENSION'

'1q gain' versus 'COMPLETENESS_OF_RESECTION'

P value = 0.0266 (Fisher's exact test), Q value = 0.24

Table S11.  Gene #2: '1q gain' versus Clinical Feature #12: 'COMPLETENESS_OF_RESECTION'

nPatients R0 R1 R2 RX
ALL 381 52 4 30
1Q GAIN MUTATED 15 6 0 4
1Q GAIN WILD-TYPE 366 46 4 26

Figure S11.  Get High-res Image Gene #2: '1q gain' versus Clinical Feature #12: 'COMPLETENESS_OF_RESECTION'

'1q gain' versus 'MULTIFOCALITY'

P value = 0.0244 (Fisher's exact test), Q value = 0.22

Table S12.  Gene #2: '1q gain' versus Clinical Feature #14: 'MULTIFOCALITY'

nPatients MULTIFOCAL UNIFOCAL
ALL 225 264
1Q GAIN MUTATED 6 20
1Q GAIN WILD-TYPE 219 244

Figure S12.  Get High-res Image Gene #2: '1q gain' versus Clinical Feature #14: 'MULTIFOCALITY'

'1q gain' versus 'TUMOR_SIZE'

P value = 0.00401 (Wilcoxon-test), Q value = 0.12

Table S13.  Gene #2: '1q gain' versus Clinical Feature #15: 'TUMOR_SIZE'

nPatients Mean (Std.Dev)
ALL 401 3.0 (1.6)
1Q GAIN MUTATED 22 3.9 (1.5)
1Q GAIN WILD-TYPE 379 2.9 (1.6)

Figure S13.  Get High-res Image Gene #2: '1q gain' versus Clinical Feature #15: 'TUMOR_SIZE'

'1q gain' versus 'RACE'

P value = 0.0025 (Fisher's exact test), Q value = 0.11

Table S14.  Gene #2: '1q gain' versus Clinical Feature #16: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 52 27 325
1Q GAIN MUTATED 1 1 5 18
1Q GAIN WILD-TYPE 0 51 22 307

Figure S14.  Get High-res Image Gene #2: '1q gain' versus Clinical Feature #16: 'RACE'

'3p gain' versus 'Time to Death'

P value = 0.00388 (logrank test), Q value = 0.12

Table S15.  Gene #3: '3p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 497 14 0.1 - 169.3 (20.4)
3P GAIN MUTATED 3 1 6.0 - 57.6 (10.7)
3P GAIN WILD-TYPE 494 13 0.1 - 169.3 (20.4)

Figure S15.  Get High-res Image Gene #3: '3p gain' versus Clinical Feature #1: 'Time to Death'

'3p gain' versus 'YEARS_TO_BIRTH'

P value = 0.0153 (Wilcoxon-test), Q value = 0.18

Table S16.  Gene #3: '3p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 499 47.2 (15.8)
3P GAIN MUTATED 3 70.3 (5.9)
3P GAIN WILD-TYPE 496 47.0 (15.7)

Figure S16.  Get High-res Image Gene #3: '3p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'3p gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.0315 (Fisher's exact test), Q value = 0.25

Table S17.  Gene #3: '3p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 277 9
3P GAIN MUTATED 0 1
3P GAIN WILD-TYPE 277 8

Figure S17.  Get High-res Image Gene #3: '3p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'3p gain' versus 'COMPLETENESS_OF_RESECTION'

P value = 0.0233 (Fisher's exact test), Q value = 0.21

Table S18.  Gene #3: '3p gain' versus Clinical Feature #12: 'COMPLETENESS_OF_RESECTION'

nPatients R0 R1 R2 RX
ALL 381 52 4 30
3P GAIN MUTATED 1 0 0 2
3P GAIN WILD-TYPE 380 52 4 28

Figure S18.  Get High-res Image Gene #3: '3p gain' versus Clinical Feature #12: 'COMPLETENESS_OF_RESECTION'

'4p gain' versus 'Time to Death'

P value = 0.011 (logrank test), Q value = 0.16

Table S19.  Gene #4: '4p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 497 14 0.1 - 169.3 (20.4)
4P GAIN MUTATED 5 1 1.0 - 57.0 (10.7)
4P GAIN WILD-TYPE 492 13 0.1 - 169.3 (20.4)

Figure S19.  Get High-res Image Gene #4: '4p gain' versus Clinical Feature #1: 'Time to Death'

'4p gain' versus 'YEARS_TO_BIRTH'

P value = 0.0295 (Wilcoxon-test), Q value = 0.25

Table S20.  Gene #4: '4p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 499 47.2 (15.8)
4P GAIN MUTATED 5 63.0 (13.3)
4P GAIN WILD-TYPE 494 47.0 (15.7)

Figure S20.  Get High-res Image Gene #4: '4p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'4p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0302 (Fisher's exact test), Q value = 0.25

Table S21.  Gene #4: '4p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 224 225
4P GAIN MUTATED 5 0
4P GAIN WILD-TYPE 219 225

Figure S21.  Get High-res Image Gene #4: '4p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'4p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0228 (Wilcoxon-test), Q value = 0.21

Table S22.  Gene #4: '4p gain' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 383 3.7 (6.2)
4P GAIN MUTATED 5 0.0 (0.0)
4P GAIN WILD-TYPE 378 3.7 (6.3)

Figure S22.  Get High-res Image Gene #4: '4p gain' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'4q gain' versus 'Time to Death'

P value = 0.011 (logrank test), Q value = 0.16

Table S23.  Gene #5: '4q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 497 14 0.1 - 169.3 (20.4)
4Q GAIN MUTATED 5 1 1.0 - 57.0 (10.7)
4Q GAIN WILD-TYPE 492 13 0.1 - 169.3 (20.4)

Figure S23.  Get High-res Image Gene #5: '4q gain' versus Clinical Feature #1: 'Time to Death'

'4q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0295 (Wilcoxon-test), Q value = 0.25

Table S24.  Gene #5: '4q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 499 47.2 (15.8)
4Q GAIN MUTATED 5 63.0 (13.3)
4Q GAIN WILD-TYPE 494 47.0 (15.7)

Figure S24.  Get High-res Image Gene #5: '4q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'4q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0302 (Fisher's exact test), Q value = 0.25

Table S25.  Gene #5: '4q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 224 225
4Q GAIN MUTATED 5 0
4Q GAIN WILD-TYPE 219 225

Figure S25.  Get High-res Image Gene #5: '4q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'4q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0228 (Wilcoxon-test), Q value = 0.21

Table S26.  Gene #5: '4q gain' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 383 3.7 (6.2)
4Q GAIN MUTATED 5 0.0 (0.0)
4Q GAIN WILD-TYPE 378 3.7 (6.3)

Figure S26.  Get High-res Image Gene #5: '4q gain' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'5p gain' versus 'YEARS_TO_BIRTH'

P value = 0.000162 (Wilcoxon-test), Q value = 0.032

Table S27.  Gene #6: '5p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 499 47.2 (15.8)
5P GAIN MUTATED 21 60.7 (15.1)
5P GAIN WILD-TYPE 478 46.6 (15.6)

Figure S27.  Get High-res Image Gene #6: '5p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'5p gain' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00396 (Fisher's exact test), Q value = 0.12

Table S28.  Gene #6: '5p gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
ALL 282 52 109 2 46 6
5P GAIN MUTATED 5 5 8 1 2 0
5P GAIN WILD-TYPE 277 47 101 1 44 6

Figure S28.  Get High-res Image Gene #6: '5p gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'5p gain' versus 'EXTRATHYROIDAL_EXTENSION'

P value = 0.0207 (Fisher's exact test), Q value = 0.2

Table S29.  Gene #6: '5p gain' versus Clinical Feature #11: 'EXTRATHYROIDAL_EXTENSION'

nPatients MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE VERY ADVANCED (T4B)
ALL 132 18 330 1
5P GAIN MUTATED 4 2 14 1
5P GAIN WILD-TYPE 128 16 316 0

Figure S29.  Get High-res Image Gene #6: '5p gain' versus Clinical Feature #11: 'EXTRATHYROIDAL_EXTENSION'

'5p gain' versus 'TUMOR_SIZE'

P value = 0.0296 (Wilcoxon-test), Q value = 0.25

Table S30.  Gene #6: '5p gain' versus Clinical Feature #15: 'TUMOR_SIZE'

nPatients Mean (Std.Dev)
ALL 401 3.0 (1.6)
5P GAIN MUTATED 20 3.7 (1.7)
5P GAIN WILD-TYPE 381 2.9 (1.6)

Figure S30.  Get High-res Image Gene #6: '5p gain' versus Clinical Feature #15: 'TUMOR_SIZE'

'5q gain' versus 'Time to Death'

P value = 0.023 (logrank test), Q value = 0.21

Table S31.  Gene #7: '5q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 497 14 0.1 - 169.3 (20.4)
5Q GAIN MUTATED 17 2 1.0 - 98.6 (20.6)
5Q GAIN WILD-TYPE 480 12 0.1 - 169.3 (20.2)

Figure S31.  Get High-res Image Gene #7: '5q gain' versus Clinical Feature #1: 'Time to Death'

'5q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0075 (Wilcoxon-test), Q value = 0.13

Table S32.  Gene #7: '5q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 499 47.2 (15.8)
5Q GAIN MUTATED 17 57.4 (14.5)
5Q GAIN WILD-TYPE 482 46.8 (15.7)

Figure S32.  Get High-res Image Gene #7: '5q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'5q gain' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00969 (Fisher's exact test), Q value = 0.15

Table S33.  Gene #7: '5q gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
ALL 282 52 109 2 46 6
5Q GAIN MUTATED 5 5 5 1 1 0
5Q GAIN WILD-TYPE 277 47 104 1 45 6

Figure S33.  Get High-res Image Gene #7: '5q gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'5q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0116 (Fisher's exact test), Q value = 0.16

Table S34.  Gene #7: '5q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 224 225
5Q GAIN MUTATED 11 2
5Q GAIN WILD-TYPE 213 223

Figure S34.  Get High-res Image Gene #7: '5q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'5q gain' versus 'EXTRATHYROIDAL_EXTENSION'

P value = 0.0173 (Fisher's exact test), Q value = 0.19

Table S35.  Gene #7: '5q gain' versus Clinical Feature #11: 'EXTRATHYROIDAL_EXTENSION'

nPatients MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE VERY ADVANCED (T4B)
ALL 132 18 330 1
5Q GAIN MUTATED 2 1 13 1
5Q GAIN WILD-TYPE 130 17 317 0

Figure S35.  Get High-res Image Gene #7: '5q gain' versus Clinical Feature #11: 'EXTRATHYROIDAL_EXTENSION'

'5q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00348 (Wilcoxon-test), Q value = 0.12

Table S36.  Gene #7: '5q gain' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 383 3.7 (6.2)
5Q GAIN MUTATED 12 0.6 (2.0)
5Q GAIN WILD-TYPE 371 3.8 (6.3)

Figure S36.  Get High-res Image Gene #7: '5q gain' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'7p gain' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0102 (Fisher's exact test), Q value = 0.16

Table S37.  Gene #8: '7p gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
ALL 282 52 109 2 46 6
7P GAIN MUTATED 7 6 3 1 1 0
7P GAIN WILD-TYPE 275 46 106 1 45 6

Figure S37.  Get High-res Image Gene #8: '7p gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'7p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00649 (Fisher's exact test), Q value = 0.13

Table S38.  Gene #8: '7p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 224 225
7P GAIN MUTATED 12 2
7P GAIN WILD-TYPE 212 223

Figure S38.  Get High-res Image Gene #8: '7p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'7p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0231 (Fisher's exact test), Q value = 0.21

Table S39.  Gene #8: '7p gain' versus Clinical Feature #8: '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 9 356 98 36
7P GAIN MUTATED 0 9 9 0
7P GAIN WILD-TYPE 9 347 89 36

Figure S39.  Get High-res Image Gene #8: '7p gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'7p gain' versus 'EXTRATHYROIDAL_EXTENSION'

P value = 0.00526 (Fisher's exact test), Q value = 0.13

Table S40.  Gene #8: '7p gain' versus Clinical Feature #11: 'EXTRATHYROIDAL_EXTENSION'

nPatients MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE VERY ADVANCED (T4B)
ALL 132 18 330 1
7P GAIN MUTATED 1 1 14 1
7P GAIN WILD-TYPE 131 17 316 0

Figure S40.  Get High-res Image Gene #8: '7p gain' versus Clinical Feature #11: 'EXTRATHYROIDAL_EXTENSION'

'7p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00196 (Wilcoxon-test), Q value = 0.098

Table S41.  Gene #8: '7p gain' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 383 3.7 (6.2)
7P GAIN MUTATED 13 0.5 (1.9)
7P GAIN WILD-TYPE 370 3.8 (6.3)

Figure S41.  Get High-res Image Gene #8: '7p gain' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'7q gain' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0179 (Fisher's exact test), Q value = 0.19

Table S42.  Gene #9: '7q gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
ALL 282 52 109 2 46 6
7Q GAIN MUTATED 8 6 4 1 1 0
7Q GAIN WILD-TYPE 274 46 105 1 45 6

Figure S42.  Get High-res Image Gene #9: '7q gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'7q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00649 (Fisher's exact test), Q value = 0.13

Table S43.  Gene #9: '7q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 224 225
7Q GAIN MUTATED 12 2
7Q GAIN WILD-TYPE 212 223

Figure S43.  Get High-res Image Gene #9: '7q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'7q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.014 (Fisher's exact test), Q value = 0.17

Table S44.  Gene #9: '7q gain' versus Clinical Feature #8: '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 9 356 98 36
7Q GAIN MUTATED 0 10 10 0
7Q GAIN WILD-TYPE 9 346 88 36

Figure S44.  Get High-res Image Gene #9: '7q gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'7q gain' versus 'EXTRATHYROIDAL_EXTENSION'

P value = 0.0188 (Fisher's exact test), Q value = 0.19

Table S45.  Gene #9: '7q gain' versus Clinical Feature #11: 'EXTRATHYROIDAL_EXTENSION'

nPatients MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE VERY ADVANCED (T4B)
ALL 132 18 330 1
7Q GAIN MUTATED 2 1 15 1
7Q GAIN WILD-TYPE 130 17 315 0

Figure S45.  Get High-res Image Gene #9: '7q gain' versus Clinical Feature #11: 'EXTRATHYROIDAL_EXTENSION'

'7q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00196 (Wilcoxon-test), Q value = 0.098

Table S46.  Gene #9: '7q gain' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 383 3.7 (6.2)
7Q GAIN MUTATED 13 0.5 (1.9)
7Q GAIN WILD-TYPE 370 3.8 (6.3)

Figure S46.  Get High-res Image Gene #9: '7q gain' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'8q gain' versus 'EXTRATHYROIDAL_EXTENSION'

P value = 0.00739 (Fisher's exact test), Q value = 0.13

Table S47.  Gene #11: '8q gain' versus Clinical Feature #11: 'EXTRATHYROIDAL_EXTENSION'

nPatients MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE VERY ADVANCED (T4B)
ALL 132 18 330 1
8Q GAIN MUTATED 0 0 6 1
8Q GAIN WILD-TYPE 132 18 324 0

Figure S47.  Get High-res Image Gene #11: '8q gain' versus Clinical Feature #11: 'EXTRATHYROIDAL_EXTENSION'

'9q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0325 (Wilcoxon-test), Q value = 0.25

Table S48.  Gene #13: '9q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 499 47.2 (15.8)
9Q GAIN MUTATED 4 62.5 (6.6)
9Q GAIN WILD-TYPE 495 47.1 (15.8)

Figure S48.  Get High-res Image Gene #13: '9q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'9q gain' versus 'TUMOR_SIZE'

P value = 0.0265 (Wilcoxon-test), Q value = 0.24

Table S49.  Gene #13: '9q gain' versus Clinical Feature #15: 'TUMOR_SIZE'

nPatients Mean (Std.Dev)
ALL 401 3.0 (1.6)
9Q GAIN MUTATED 4 4.5 (0.6)
9Q GAIN WILD-TYPE 397 3.0 (1.6)

Figure S49.  Get High-res Image Gene #13: '9q gain' versus Clinical Feature #15: 'TUMOR_SIZE'

'12p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.000862 (Fisher's exact test), Q value = 0.062

Table S50.  Gene #16: '12p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 224 225
12P GAIN MUTATED 10 0
12P GAIN WILD-TYPE 214 225

Figure S50.  Get High-res Image Gene #16: '12p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'12p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0155 (Fisher's exact test), Q value = 0.18

Table S51.  Gene #16: '12p gain' versus Clinical Feature #8: '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 9 356 98 36
12P GAIN MUTATED 0 6 8 0
12P GAIN WILD-TYPE 9 350 90 36

Figure S51.  Get High-res Image Gene #16: '12p gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'12p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00119 (Wilcoxon-test), Q value = 0.074

Table S52.  Gene #16: '12p gain' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 383 3.7 (6.2)
12P GAIN MUTATED 10 0.0 (0.0)
12P GAIN WILD-TYPE 373 3.8 (6.3)

Figure S52.  Get High-res Image Gene #16: '12p gain' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'12q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.000862 (Fisher's exact test), Q value = 0.062

Table S53.  Gene #17: '12q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 224 225
12Q GAIN MUTATED 10 0
12Q GAIN WILD-TYPE 214 225

Figure S53.  Get High-res Image Gene #17: '12q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'12q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00615 (Fisher's exact test), Q value = 0.13

Table S54.  Gene #17: '12q gain' versus Clinical Feature #8: '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 9 356 98 36
12Q GAIN MUTATED 0 6 9 0
12Q GAIN WILD-TYPE 9 350 89 36

Figure S54.  Get High-res Image Gene #17: '12q gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'12q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00119 (Wilcoxon-test), Q value = 0.074

Table S55.  Gene #17: '12q gain' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 383 3.7 (6.2)
12Q GAIN MUTATED 10 0.0 (0.0)
12Q GAIN WILD-TYPE 373 3.8 (6.3)

Figure S55.  Get High-res Image Gene #17: '12q gain' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'14q gain' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00703 (Fisher's exact test), Q value = 0.13

Table S56.  Gene #19: '14q gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
ALL 282 52 109 2 46 6
14Q GAIN MUTATED 2 5 4 0 0 0
14Q GAIN WILD-TYPE 280 47 105 2 46 6

Figure S56.  Get High-res Image Gene #19: '14q gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'16p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0108 (Fisher's exact test), Q value = 0.16

Table S57.  Gene #20: '16p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 224 225
16P GAIN MUTATED 9 1
16P GAIN WILD-TYPE 215 224

Figure S57.  Get High-res Image Gene #20: '16p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'16p gain' versus 'EXTRATHYROIDAL_EXTENSION'

P value = 0.0255 (Fisher's exact test), Q value = 0.23

Table S58.  Gene #20: '16p gain' versus Clinical Feature #11: 'EXTRATHYROIDAL_EXTENSION'

nPatients MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE VERY ADVANCED (T4B)
ALL 132 18 330 1
16P GAIN MUTATED 2 0 12 1
16P GAIN WILD-TYPE 130 18 318 0

Figure S58.  Get High-res Image Gene #20: '16p gain' versus Clinical Feature #11: 'EXTRATHYROIDAL_EXTENSION'

'16p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00213 (Wilcoxon-test), Q value = 0.1

Table S59.  Gene #20: '16p gain' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 383 3.7 (6.2)
16P GAIN MUTATED 9 0.0 (0.0)
16P GAIN WILD-TYPE 374 3.8 (6.3)

Figure S59.  Get High-res Image Gene #20: '16p gain' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'16q gain' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0218 (Fisher's exact test), Q value = 0.21

Table S60.  Gene #21: '16q gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
ALL 282 52 109 2 46 6
16Q GAIN MUTATED 6 4 2 1 0 0
16Q GAIN WILD-TYPE 276 48 107 1 46 6

Figure S60.  Get High-res Image Gene #21: '16q gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'16q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0201 (Fisher's exact test), Q value = 0.2

Table S61.  Gene #21: '16q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 224 225
16Q GAIN MUTATED 8 1
16Q GAIN WILD-TYPE 216 224

Figure S61.  Get High-res Image Gene #21: '16q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'16q gain' versus 'EXTRATHYROIDAL_EXTENSION'

P value = 0.0137 (Fisher's exact test), Q value = 0.17

Table S62.  Gene #21: '16q gain' versus Clinical Feature #11: 'EXTRATHYROIDAL_EXTENSION'

nPatients MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE VERY ADVANCED (T4B)
ALL 132 18 330 1
16Q GAIN MUTATED 1 0 11 1
16Q GAIN WILD-TYPE 131 18 319 0

Figure S62.  Get High-res Image Gene #21: '16q gain' versus Clinical Feature #11: 'EXTRATHYROIDAL_EXTENSION'

'16q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00383 (Wilcoxon-test), Q value = 0.12

Table S63.  Gene #21: '16q gain' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 383 3.7 (6.2)
16Q GAIN MUTATED 8 0.0 (0.0)
16Q GAIN WILD-TYPE 375 3.8 (6.3)

Figure S63.  Get High-res Image Gene #21: '16q gain' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'17p gain' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00427 (Fisher's exact test), Q value = 0.12

Table S64.  Gene #22: '17p gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
ALL 282 52 109 2 46 6
17P GAIN MUTATED 6 6 3 1 0 0
17P GAIN WILD-TYPE 276 46 106 1 46 6

Figure S64.  Get High-res Image Gene #22: '17p gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'17p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0206 (Fisher's exact test), Q value = 0.2

Table S65.  Gene #22: '17p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 224 225
17P GAIN MUTATED 10 2
17P GAIN WILD-TYPE 214 223

Figure S65.  Get High-res Image Gene #22: '17p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'17p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0177 (Wilcoxon-test), Q value = 0.19

Table S66.  Gene #22: '17p gain' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 383 3.7 (6.2)
17P GAIN MUTATED 11 0.6 (1.4)
17P GAIN WILD-TYPE 372 3.8 (6.3)

Figure S66.  Get High-res Image Gene #22: '17p gain' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'17q gain' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0106 (Fisher's exact test), Q value = 0.16

Table S67.  Gene #23: '17q gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
ALL 282 52 109 2 46 6
17Q GAIN MUTATED 7 6 3 1 1 0
17Q GAIN WILD-TYPE 275 46 106 1 45 6

Figure S67.  Get High-res Image Gene #23: '17q gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'17q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0322 (Fisher's exact test), Q value = 0.25

Table S68.  Gene #23: '17q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 224 225
17Q GAIN MUTATED 11 3
17Q GAIN WILD-TYPE 213 222

Figure S68.  Get High-res Image Gene #23: '17q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'17q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0321 (Wilcoxon-test), Q value = 0.25

Table S69.  Gene #23: '17q gain' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 383 3.7 (6.2)
17Q GAIN MUTATED 13 1.1 (2.2)
17Q GAIN WILD-TYPE 370 3.8 (6.3)

Figure S69.  Get High-res Image Gene #23: '17q gain' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'18p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0302 (Fisher's exact test), Q value = 0.25

Table S70.  Gene #24: '18p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 224 225
18P GAIN MUTATED 5 0
18P GAIN WILD-TYPE 219 225

Figure S70.  Get High-res Image Gene #24: '18p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'18q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0302 (Fisher's exact test), Q value = 0.25

Table S71.  Gene #25: '18q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 224 225
18Q GAIN MUTATED 5 0
18Q GAIN WILD-TYPE 219 225

Figure S71.  Get High-res Image Gene #25: '18q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'19p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0149 (Fisher's exact test), Q value = 0.17

Table S72.  Gene #26: '19p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 224 225
19P GAIN MUTATED 6 0
19P GAIN WILD-TYPE 218 225

Figure S72.  Get High-res Image Gene #26: '19p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'19p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0079 (Fisher's exact test), Q value = 0.14

Table S73.  Gene #26: '19p gain' versus Clinical Feature #8: '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 9 356 98 36
19P GAIN MUTATED 0 2 6 0
19P GAIN WILD-TYPE 9 354 92 36

Figure S73.  Get High-res Image Gene #26: '19p gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'19p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0125 (Wilcoxon-test), Q value = 0.17

Table S74.  Gene #26: '19p gain' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 383 3.7 (6.2)
19P GAIN MUTATED 6 0.0 (0.0)
19P GAIN WILD-TYPE 377 3.7 (6.3)

Figure S74.  Get High-res Image Gene #26: '19p gain' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'19q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0158 (Wilcoxon-test), Q value = 0.18

Table S75.  Gene #27: '19q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 499 47.2 (15.8)
19Q GAIN MUTATED 10 59.8 (15.6)
19Q GAIN WILD-TYPE 489 46.9 (15.7)

Figure S75.  Get High-res Image Gene #27: '19q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'19q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00733 (Fisher's exact test), Q value = 0.13

Table S76.  Gene #27: '19q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 224 225
19Q GAIN MUTATED 7 0
19Q GAIN WILD-TYPE 217 225

Figure S76.  Get High-res Image Gene #27: '19q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'19q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00463 (Fisher's exact test), Q value = 0.13

Table S77.  Gene #27: '19q gain' versus Clinical Feature #8: '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 9 356 98 36
19Q GAIN MUTATED 0 3 7 0
19Q GAIN WILD-TYPE 9 353 91 36

Figure S77.  Get High-res Image Gene #27: '19q gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'19q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00691 (Wilcoxon-test), Q value = 0.13

Table S78.  Gene #27: '19q gain' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 383 3.7 (6.2)
19Q GAIN MUTATED 7 0.0 (0.0)
19Q GAIN WILD-TYPE 376 3.7 (6.3)

Figure S78.  Get High-res Image Gene #27: '19q gain' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'20p gain' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00982 (Fisher's exact test), Q value = 0.15

Table S79.  Gene #28: '20p gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
ALL 282 52 109 2 46 6
20P GAIN MUTATED 4 4 3 1 0 0
20P GAIN WILD-TYPE 278 48 106 1 46 6

Figure S79.  Get High-res Image Gene #28: '20p gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'20p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00401 (Fisher's exact test), Q value = 0.12

Table S80.  Gene #28: '20p gain' versus Clinical Feature #8: '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 9 356 98 36
20P GAIN MUTATED 0 4 8 0
20P GAIN WILD-TYPE 9 352 90 36

Figure S80.  Get High-res Image Gene #28: '20p gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'20p gain' versus 'EXTRATHYROIDAL_EXTENSION'

P value = 0.014 (Fisher's exact test), Q value = 0.17

Table S81.  Gene #28: '20p gain' versus Clinical Feature #11: 'EXTRATHYROIDAL_EXTENSION'

nPatients MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE VERY ADVANCED (T4B)
ALL 132 18 330 1
20P GAIN MUTATED 1 0 10 1
20P GAIN WILD-TYPE 131 18 320 0

Figure S81.  Get High-res Image Gene #28: '20p gain' versus Clinical Feature #11: 'EXTRATHYROIDAL_EXTENSION'

'20p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00691 (Wilcoxon-test), Q value = 0.13

Table S82.  Gene #28: '20p gain' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 383 3.7 (6.2)
20P GAIN MUTATED 7 0.0 (0.0)
20P GAIN WILD-TYPE 376 3.7 (6.3)

Figure S82.  Get High-res Image Gene #28: '20p gain' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'20q gain' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0103 (Fisher's exact test), Q value = 0.16

Table S83.  Gene #29: '20q gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
ALL 282 52 109 2 46 6
20Q GAIN MUTATED 4 4 3 1 0 0
20Q GAIN WILD-TYPE 278 48 106 1 46 6

Figure S83.  Get High-res Image Gene #29: '20q gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'20q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00421 (Fisher's exact test), Q value = 0.12

Table S84.  Gene #29: '20q gain' versus Clinical Feature #8: '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 9 356 98 36
20Q GAIN MUTATED 0 4 8 0
20Q GAIN WILD-TYPE 9 352 90 36

Figure S84.  Get High-res Image Gene #29: '20q gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'20q gain' versus 'EXTRATHYROIDAL_EXTENSION'

P value = 0.0136 (Fisher's exact test), Q value = 0.17

Table S85.  Gene #29: '20q gain' versus Clinical Feature #11: 'EXTRATHYROIDAL_EXTENSION'

nPatients MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE VERY ADVANCED (T4B)
ALL 132 18 330 1
20Q GAIN MUTATED 1 0 10 1
20Q GAIN WILD-TYPE 131 18 320 0

Figure S85.  Get High-res Image Gene #29: '20q gain' versus Clinical Feature #11: 'EXTRATHYROIDAL_EXTENSION'

'20q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00691 (Wilcoxon-test), Q value = 0.13

Table S86.  Gene #29: '20q gain' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 383 3.7 (6.2)
20Q GAIN MUTATED 7 0.0 (0.0)
20Q GAIN WILD-TYPE 376 3.7 (6.3)

Figure S86.  Get High-res Image Gene #29: '20q gain' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'xp gain' versus 'YEARS_TO_BIRTH'

P value = 0.0138 (Wilcoxon-test), Q value = 0.17

Table S87.  Gene #31: 'xp gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 499 47.2 (15.8)
XP GAIN MUTATED 8 60.0 (10.9)
XP GAIN WILD-TYPE 491 47.0 (15.8)

Figure S87.  Get High-res Image Gene #31: 'xp gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'xp gain' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0081 (Fisher's exact test), Q value = 0.14

Table S88.  Gene #31: 'xp gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
ALL 282 52 109 2 46 6
XP GAIN MUTATED 2 3 2 1 0 0
XP GAIN WILD-TYPE 280 49 107 1 46 6

Figure S88.  Get High-res Image Gene #31: 'xp gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'xp gain' versus 'EXTRATHYROIDAL_EXTENSION'

P value = 0.0177 (Fisher's exact test), Q value = 0.19

Table S89.  Gene #31: 'xp gain' versus Clinical Feature #11: 'EXTRATHYROIDAL_EXTENSION'

nPatients MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE VERY ADVANCED (T4B)
ALL 132 18 330 1
XP GAIN MUTATED 1 0 6 1
XP GAIN WILD-TYPE 131 18 324 0

Figure S89.  Get High-res Image Gene #31: 'xp gain' versus Clinical Feature #11: 'EXTRATHYROIDAL_EXTENSION'

'xp gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0125 (Wilcoxon-test), Q value = 0.17

Table S90.  Gene #31: 'xp gain' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 383 3.7 (6.2)
XP GAIN MUTATED 6 0.0 (0.0)
XP GAIN WILD-TYPE 377 3.7 (6.3)

Figure S90.  Get High-res Image Gene #31: 'xp gain' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'xq gain' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0146 (Fisher's exact test), Q value = 0.17

Table S91.  Gene #32: 'xq gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
ALL 282 52 109 2 46 6
XQ GAIN MUTATED 3 3 2 1 0 0
XQ GAIN WILD-TYPE 279 49 107 1 46 6

Figure S91.  Get High-res Image Gene #32: 'xq gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'xq gain' versus 'EXTRATHYROIDAL_EXTENSION'

P value = 0.0189 (Fisher's exact test), Q value = 0.19

Table S92.  Gene #32: 'xq gain' versus Clinical Feature #11: 'EXTRATHYROIDAL_EXTENSION'

nPatients MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE VERY ADVANCED (T4B)
ALL 132 18 330 1
XQ GAIN MUTATED 1 0 7 1
XQ GAIN WILD-TYPE 131 18 323 0

Figure S92.  Get High-res Image Gene #32: 'xq gain' versus Clinical Feature #11: 'EXTRATHYROIDAL_EXTENSION'

'2p loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0307 (Fisher's exact test), Q value = 0.25

Table S93.  Gene #35: '2p loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
ALL 282 52 109 2 46 6
2P LOSS MUTATED 4 5 1 0 0 0
2P LOSS WILD-TYPE 278 47 108 2 46 6

Figure S93.  Get High-res Image Gene #35: '2p loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'2p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0036 (Fisher's exact test), Q value = 0.12

Table S94.  Gene #35: '2p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 224 225
2P LOSS MUTATED 8 0
2P LOSS WILD-TYPE 216 225

Figure S94.  Get High-res Image Gene #35: '2p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'2p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00485 (Fisher's exact test), Q value = 0.13

Table S95.  Gene #35: '2p loss' versus Clinical Feature #8: '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 9 356 98 36
2P LOSS MUTATED 0 3 7 0
2P LOSS WILD-TYPE 9 353 91 36

Figure S95.  Get High-res Image Gene #35: '2p loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'2p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00383 (Wilcoxon-test), Q value = 0.12

Table S96.  Gene #35: '2p loss' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 383 3.7 (6.2)
2P LOSS MUTATED 8 0.0 (0.0)
2P LOSS WILD-TYPE 375 3.8 (6.3)

Figure S96.  Get High-res Image Gene #35: '2p loss' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'2q loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0307 (Fisher's exact test), Q value = 0.25

Table S97.  Gene #36: '2q loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
ALL 282 52 109 2 46 6
2Q LOSS MUTATED 4 5 1 0 0 0
2Q LOSS WILD-TYPE 278 47 108 2 46 6

Figure S97.  Get High-res Image Gene #36: '2q loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'2q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00733 (Fisher's exact test), Q value = 0.13

Table S98.  Gene #36: '2q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 224 225
2Q LOSS MUTATED 7 0
2Q LOSS WILD-TYPE 217 225

Figure S98.  Get High-res Image Gene #36: '2q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'2q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00517 (Fisher's exact test), Q value = 0.13

Table S99.  Gene #36: '2q loss' versus Clinical Feature #8: '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 9 356 98 36
2Q LOSS MUTATED 0 3 7 0
2Q LOSS WILD-TYPE 9 353 91 36

Figure S99.  Get High-res Image Gene #36: '2q loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'2q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00691 (Wilcoxon-test), Q value = 0.13

Table S100.  Gene #36: '2q loss' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 383 3.7 (6.2)
2Q LOSS MUTATED 7 0.0 (0.0)
2Q LOSS WILD-TYPE 376 3.7 (6.3)

Figure S100.  Get High-res Image Gene #36: '2q loss' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'6q loss' versus 'Time to Death'

P value = 0.00192 (logrank test), Q value = 0.098

Table S101.  Gene #40: '6q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 497 14 0.1 - 169.3 (20.4)
6Q LOSS MUTATED 6 2 7.8 - 98.6 (37.9)
6Q LOSS WILD-TYPE 491 12 0.1 - 169.3 (20.2)

Figure S101.  Get High-res Image Gene #40: '6q loss' versus Clinical Feature #1: 'Time to Death'

'6q loss' versus 'TUMOR_SIZE'

P value = 0.00963 (Wilcoxon-test), Q value = 0.15

Table S102.  Gene #40: '6q loss' versus Clinical Feature #15: 'TUMOR_SIZE'

nPatients Mean (Std.Dev)
ALL 401 3.0 (1.6)
6Q LOSS MUTATED 6 4.6 (1.2)
6Q LOSS WILD-TYPE 395 3.0 (1.6)

Figure S102.  Get High-res Image Gene #40: '6q loss' versus Clinical Feature #15: 'TUMOR_SIZE'

'9p loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0274 (Fisher's exact test), Q value = 0.24

Table S103.  Gene #43: '9p loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
ALL 282 52 109 2 46 6
9P LOSS MUTATED 8 4 4 1 1 1
9P LOSS WILD-TYPE 274 48 105 1 45 5

Figure S103.  Get High-res Image Gene #43: '9p loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'9q loss' versus 'YEARS_TO_BIRTH'

P value = 0.000793 (Wilcoxon-test), Q value = 0.062

Table S104.  Gene #44: '9q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 499 47.2 (15.8)
9Q LOSS MUTATED 25 58.9 (18.2)
9Q LOSS WILD-TYPE 474 46.6 (15.4)

Figure S104.  Get High-res Image Gene #44: '9q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'9q loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00042 (Fisher's exact test), Q value = 0.06

Table S105.  Gene #44: '9q loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
ALL 282 52 109 2 46 6
9Q LOSS MUTATED 9 5 4 2 4 1
9Q LOSS WILD-TYPE 273 47 105 0 42 5

Figure S105.  Get High-res Image Gene #44: '9q loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'10p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0149 (Fisher's exact test), Q value = 0.17

Table S106.  Gene #45: '10p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 224 225
10P LOSS MUTATED 6 0
10P LOSS WILD-TYPE 218 225

Figure S106.  Get High-res Image Gene #45: '10p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'10p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0228 (Wilcoxon-test), Q value = 0.21

Table S107.  Gene #45: '10p loss' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 383 3.7 (6.2)
10P LOSS MUTATED 5 0.0 (0.0)
10P LOSS WILD-TYPE 378 3.7 (6.3)

Figure S107.  Get High-res Image Gene #45: '10p loss' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'10p loss' versus 'TUMOR_SIZE'

P value = 0.0119 (Wilcoxon-test), Q value = 0.17

Table S108.  Gene #45: '10p loss' versus Clinical Feature #15: 'TUMOR_SIZE'

nPatients Mean (Std.Dev)
ALL 401 3.0 (1.6)
10P LOSS MUTATED 6 4.8 (1.8)
10P LOSS WILD-TYPE 395 3.0 (1.6)

Figure S108.  Get High-res Image Gene #45: '10p loss' versus Clinical Feature #15: 'TUMOR_SIZE'

'10q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0302 (Fisher's exact test), Q value = 0.25

Table S109.  Gene #46: '10q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 224 225
10Q LOSS MUTATED 5 0
10Q LOSS WILD-TYPE 219 225

Figure S109.  Get High-res Image Gene #46: '10q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'10q loss' versus 'TUMOR_SIZE'

P value = 0.00858 (Wilcoxon-test), Q value = 0.14

Table S110.  Gene #46: '10q loss' versus Clinical Feature #15: 'TUMOR_SIZE'

nPatients Mean (Std.Dev)
ALL 401 3.0 (1.6)
10Q LOSS MUTATED 5 5.1 (1.7)
10Q LOSS WILD-TYPE 396 3.0 (1.6)

Figure S110.  Get High-res Image Gene #46: '10q loss' versus Clinical Feature #15: 'TUMOR_SIZE'

'11p loss' versus 'Time to Death'

P value = 0.00266 (logrank test), Q value = 0.11

Table S111.  Gene #47: '11p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 497 14 0.1 - 169.3 (20.4)
11P LOSS MUTATED 7 1 1.4 - 44.1 (20.6)
11P LOSS WILD-TYPE 490 13 0.1 - 169.3 (20.3)

Figure S111.  Get High-res Image Gene #47: '11p loss' versus Clinical Feature #1: 'Time to Death'

'11p loss' versus 'YEARS_TO_BIRTH'

P value = 0.000665 (Wilcoxon-test), Q value = 0.061

Table S112.  Gene #47: '11p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 499 47.2 (15.8)
11P LOSS MUTATED 7 68.1 (8.7)
11P LOSS WILD-TYPE 492 46.9 (15.7)

Figure S112.  Get High-res Image Gene #47: '11p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'11p loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00544 (Fisher's exact test), Q value = 0.13

Table S113.  Gene #47: '11p loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
ALL 282 52 109 2 46 6
11P LOSS MUTATED 1 1 4 1 0 0
11P LOSS WILD-TYPE 281 51 105 1 46 6

Figure S113.  Get High-res Image Gene #47: '11p loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'11p loss' versus 'GENDER'

P value = 0.0164 (Fisher's exact test), Q value = 0.18

Table S114.  Gene #47: '11p loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 366 133
11P LOSS MUTATED 2 5
11P LOSS WILD-TYPE 364 128

Figure S114.  Get High-res Image Gene #47: '11p loss' versus Clinical Feature #7: 'GENDER'

'11p loss' versus 'TUMOR_SIZE'

P value = 0.00797 (Wilcoxon-test), Q value = 0.14

Table S115.  Gene #47: '11p loss' versus Clinical Feature #15: 'TUMOR_SIZE'

nPatients Mean (Std.Dev)
ALL 401 3.0 (1.6)
11P LOSS MUTATED 7 4.9 (1.9)
11P LOSS WILD-TYPE 394 2.9 (1.6)

Figure S115.  Get High-res Image Gene #47: '11p loss' versus Clinical Feature #15: 'TUMOR_SIZE'

'11q loss' versus 'Time to Death'

P value = 0.0054 (logrank test), Q value = 0.13

Table S116.  Gene #48: '11q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 497 14 0.1 - 169.3 (20.4)
11Q LOSS MUTATED 9 1 1.4 - 44.1 (20.6)
11Q LOSS WILD-TYPE 488 13 0.1 - 169.3 (20.3)

Figure S116.  Get High-res Image Gene #48: '11q loss' versus Clinical Feature #1: 'Time to Death'

'11q loss' versus 'YEARS_TO_BIRTH'

P value = 0.000199 (Wilcoxon-test), Q value = 0.033

Table S117.  Gene #48: '11q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 499 47.2 (15.8)
11Q LOSS MUTATED 9 67.0 (8.9)
11Q LOSS WILD-TYPE 490 46.8 (15.7)

Figure S117.  Get High-res Image Gene #48: '11q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'11q loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00357 (Fisher's exact test), Q value = 0.12

Table S118.  Gene #48: '11q loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
ALL 282 52 109 2 46 6
11Q LOSS MUTATED 1 2 4 1 1 0
11Q LOSS WILD-TYPE 281 50 105 1 45 6

Figure S118.  Get High-res Image Gene #48: '11q loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'11q loss' versus 'GENDER'

P value = 0.00184 (Fisher's exact test), Q value = 0.098

Table S119.  Gene #48: '11q loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 366 133
11Q LOSS MUTATED 2 7
11Q LOSS WILD-TYPE 364 126

Figure S119.  Get High-res Image Gene #48: '11q loss' versus Clinical Feature #7: 'GENDER'

'11q loss' versus 'TUMOR_SIZE'

P value = 0.00239 (Wilcoxon-test), Q value = 0.11

Table S120.  Gene #48: '11q loss' versus Clinical Feature #15: 'TUMOR_SIZE'

nPatients Mean (Std.Dev)
ALL 401 3.0 (1.6)
11Q LOSS MUTATED 8 5.0 (1.8)
11Q LOSS WILD-TYPE 393 2.9 (1.6)

Figure S120.  Get High-res Image Gene #48: '11q loss' versus Clinical Feature #15: 'TUMOR_SIZE'

'13q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0299 (Wilcoxon-test), Q value = 0.25

Table S121.  Gene #49: '13q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 499 47.2 (15.8)
13Q LOSS MUTATED 14 56.5 (16.1)
13Q LOSS WILD-TYPE 485 46.9 (15.7)

Figure S121.  Get High-res Image Gene #49: '13q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'13q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00572 (Fisher's exact test), Q value = 0.13

Table S122.  Gene #49: '13q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 224 225
13Q LOSS MUTATED 10 1
13Q LOSS WILD-TYPE 214 224

Figure S122.  Get High-res Image Gene #49: '13q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'13q loss' versus 'RADIATION_EXPOSURE'

P value = 0.000641 (Fisher's exact test), Q value = 0.061

Table S123.  Gene #49: '13q loss' versus Clinical Feature #10: 'RADIATION_EXPOSURE'

nPatients NO YES
ALL 421 17
13Q LOSS MUTATED 8 4
13Q LOSS WILD-TYPE 413 13

Figure S123.  Get High-res Image Gene #49: '13q loss' versus Clinical Feature #10: 'RADIATION_EXPOSURE'

'13q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0161 (Wilcoxon-test), Q value = 0.18

Table S124.  Gene #49: '13q loss' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 383 3.7 (6.2)
13Q LOSS MUTATED 8 0.2 (0.7)
13Q LOSS WILD-TYPE 375 3.8 (6.3)

Figure S124.  Get High-res Image Gene #49: '13q loss' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'17p loss' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.0186 (Fisher's exact test), Q value = 0.19

Table S125.  Gene #51: '17p loss' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 14 485
17P LOSS MUTATED 2 6
17P LOSS WILD-TYPE 12 479

Figure S125.  Get High-res Image Gene #51: '17p loss' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'17p loss' versus 'TUMOR_SIZE'

P value = 0.0149 (Wilcoxon-test), Q value = 0.17

Table S126.  Gene #51: '17p loss' versus Clinical Feature #15: 'TUMOR_SIZE'

nPatients Mean (Std.Dev)
ALL 401 3.0 (1.6)
17P LOSS MUTATED 7 4.5 (1.6)
17P LOSS WILD-TYPE 394 3.0 (1.6)

Figure S126.  Get High-res Image Gene #51: '17p loss' versus Clinical Feature #15: 'TUMOR_SIZE'

'19p loss' versus 'RADIATION_EXPOSURE'

P value = 0.0133 (Fisher's exact test), Q value = 0.17

Table S127.  Gene #55: '19p loss' versus Clinical Feature #10: 'RADIATION_EXPOSURE'

nPatients NO YES
ALL 421 17
19P LOSS MUTATED 3 2
19P LOSS WILD-TYPE 418 15

Figure S127.  Get High-res Image Gene #55: '19p loss' versus Clinical Feature #10: 'RADIATION_EXPOSURE'

'19p loss' versus 'TUMOR_SIZE'

P value = 0.00941 (Wilcoxon-test), Q value = 0.15

Table S128.  Gene #55: '19p loss' versus Clinical Feature #15: 'TUMOR_SIZE'

nPatients Mean (Std.Dev)
ALL 401 3.0 (1.6)
19P LOSS MUTATED 3 5.8 (0.8)
19P LOSS WILD-TYPE 398 3.0 (1.6)

Figure S128.  Get High-res Image Gene #55: '19p loss' versus Clinical Feature #15: 'TUMOR_SIZE'

'21q loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0135 (Fisher's exact test), Q value = 0.17

Table S129.  Gene #56: '21q loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
ALL 282 52 109 2 46 6
21Q LOSS MUTATED 1 4 2 0 1 0
21Q LOSS WILD-TYPE 281 48 107 2 45 6

Figure S129.  Get High-res Image Gene #56: '21q loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'xp loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0316 (Fisher's exact test), Q value = 0.25

Table S130.  Gene #58: 'xp loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
ALL 282 52 109 2 46 6
XP LOSS MUTATED 1 3 0 0 0 0
XP LOSS WILD-TYPE 281 49 109 2 46 6

Figure S130.  Get High-res Image Gene #58: 'xp loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'xq loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00597 (Fisher's exact test), Q value = 0.13

Table S131.  Gene #59: 'xq loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
ALL 282 52 109 2 46 6
XQ LOSS MUTATED 0 3 0 0 0 0
XQ LOSS WILD-TYPE 282 49 109 2 46 6

Figure S131.  Get High-res Image Gene #59: 'xq loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

Methods & Data
Input

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

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/THCA-TP/15101916/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/THCA-TP/15092795/THCA-TP.merged_data.txt

  • Number of patients = 499

  • Number of significantly arm-level cnvs = 59

  • 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.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)
[2] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[3] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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