Correlation between copy number variations of arm-level result and selected clinical features
Thyroid Adenocarcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlation between copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1P55N16
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, 110 significant findings detected with Q value < 0.25.

  • 1p gain cnv correlated to 'PATHOLOGIC_STAGE'.

  • 1q gain cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'HISTOLOGICAL_TYPE',  'EXTRATHYROIDAL_EXTENSION',  'TUMOR_SIZE', and 'RACE'.

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

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

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

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

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

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

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

  • 8q gain cnv correlated to 'EXTRATHYROIDAL_EXTENSION'.

  • 9q gain cnv correlated to '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 'PATHOLOGIC_STAGE'.

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

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

  • 17p gain cnv correlated to 'PATHOLOGIC_STAGE' and 'NUMBER_OF_LYMPH_NODES'.

  • 17q gain cnv correlated to 'PATHOLOGIC_STAGE'.

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

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

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

  • xq gain cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGIC_STAGE',  'EXTRATHYROIDAL_EXTENSION', and 'NUMBER_OF_LYMPH_NODES'.

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

  • 2q loss cnv correlated to 'PATHOLOGIC_STAGE',  '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 'PATHOLOGIC_STAGE'.

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

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

  • 10q loss cnv correlated to 'TUMOR_SIZE'.

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

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

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

  • 17p loss cnv correlated to 'TUMOR_SIZE'.

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

  • 21q loss cnv correlated to 'PATHOLOGIC_STAGE'.

  • xp loss cnv correlated to 'PATHOLOGIC_STAGE'.

  • xq loss cnv correlated to 'PATHOLOGIC_STAGE'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 59 arm-level events and 17 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 110 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
1q gain 26 (5%) 473 0.203
(0.759)
3.58e-05
(0.012)
3e-05
(0.012)
1e-05
(0.01)
0.00186
(0.0983)
1
(1.00)
0.652
(1.00)
0.127
(0.594)
0.0169
(0.198)
1
(1.00)
5e-05
(0.0125)
0.0511
(0.369)
0.0584
(0.386)
0.0669
(0.405)
0.00846
(0.154)
0.00206
(0.0983)
0.269
(0.869)
5q gain 17 (3%) 482 0.0154
(0.192)
0.00787
(0.154)
0.00913
(0.154)
0.35
(0.969)
0.0206
(0.218)
1
(1.00)
0.413
(1.00)
0.585
(1.00)
0.063
(0.395)
1
(1.00)
0.0176
(0.201)
0.359
(0.985)
0.00337
(0.126)
1
(1.00)
0.0703
(0.418)
0.559
(1.00)
0.608
(1.00)
7q gain 20 (4%) 479 0.478
(1.00)
0.0391
(0.31)
0.0155
(0.192)
0.562
(1.00)
0.0116
(0.176)
1
(1.00)
1
(1.00)
0.447
(1.00)
0.016
(0.196)
1
(1.00)
0.0181
(0.203)
0.21
(0.776)
0.00189
(0.0983)
1
(1.00)
0.364
(0.993)
0.487
(1.00)
0.608
(1.00)
11p loss 7 (1%) 492 0.0167
(0.198)
0.000675
(0.0752)
0.00613
(0.151)
0.235
(0.816)
0.449
(1.00)
1
(1.00)
0.017
(0.198)
0.419
(1.00)
0.815
(1.00)
1
(1.00)
0.558
(1.00)
0.525
(1.00)
0.208
(0.773)
0.708
(1.00)
0.00751
(0.154)
0.474
(1.00)
1
(1.00)
11q loss 9 (2%) 490 0.0258
(0.24)
0.000203
(0.034)
0.00349
(0.126)
0.223
(0.794)
0.503
(1.00)
1
(1.00)
0.00193
(0.0983)
0.268
(0.869)
1
(1.00)
1
(1.00)
0.805
(1.00)
0.513
(1.00)
0.316
(0.941)
1
(1.00)
0.00222
(0.0983)
0.541
(1.00)
1
(1.00)
5p gain 21 (4%) 478 0.0783
(0.439)
0.000172
(0.034)
0.00363
(0.126)
0.256
(0.846)
0.323
(0.948)
1
(1.00)
0.461
(1.00)
0.465
(1.00)
0.163
(0.685)
1
(1.00)
0.021
(0.22)
0.395
(1.00)
0.0708
(0.418)
0.509
(1.00)
0.0269
(0.246)
0.405
(1.00)
1
(1.00)
7p gain 18 (4%) 481 0.388
(1.00)
0.0465
(0.343)
0.00919
(0.154)
0.42
(1.00)
0.0116
(0.176)
1
(1.00)
1
(1.00)
0.793
(1.00)
0.0278
(0.251)
1
(1.00)
0.00562
(0.151)
0.36
(0.988)
0.00189
(0.0983)
1
(1.00)
0.349
(0.969)
0.556
(1.00)
0.608
(1.00)
19q gain 10 (2%) 489 0.0468
(0.343)
0.0163
(0.196)
0.616
(1.00)
0.337
(0.953)
0.0149
(0.192)
0.142
(0.635)
0.495
(1.00)
0.00514
(0.15)
1
(1.00)
0.532
(1.00)
0.689
(1.00)
0.00663
(0.151)
0.524
(1.00)
0.0799
(0.443)
1
(1.00)
1
(1.00)
20p gain 12 (2%) 487 0.254
(0.843)
0.0847
(0.457)
0.00923
(0.154)
0.58
(1.00)
0.0679
(0.405)
0.742
(1.00)
0.751
(1.00)
0.0044
(0.147)
1
(1.00)
0.0134
(0.19)
0.857
(1.00)
0.00663
(0.151)
0.779
(1.00)
0.0914
(0.478)
1
(1.00)
1
(1.00)
20q gain 12 (2%) 487 0.254
(0.843)
0.0847
(0.457)
0.00946
(0.154)
0.578
(1.00)
0.0679
(0.405)
0.742
(1.00)
0.751
(1.00)
0.00457
(0.148)
1
(1.00)
0.0137
(0.191)
0.856
(1.00)
0.00663
(0.151)
0.779
(1.00)
0.0914
(0.478)
1
(1.00)
1
(1.00)
xp gain 8 (2%) 491 0.0877
(0.468)
0.0142
(0.192)
0.00746
(0.154)
0.31
(0.936)
0.122
(0.581)
1
(1.00)
0.688
(1.00)
1
(1.00)
0.223
(0.794)
0.274
(0.875)
0.0182
(0.203)
0.0508
(0.369)
0.0121
(0.176)
0.48
(1.00)
0.456
(1.00)
1
(1.00)
1
(1.00)
xq gain 7 (1%) 492 0.0562
(0.386)
0.027
(0.246)
0.0189
(0.206)
0.395
(1.00)
0.216
(0.789)
1
(1.00)
0.198
(0.746)
1
(1.00)
0.154
(0.662)
1
(1.00)
0.0186
(0.206)
0.191
(0.724)
0.0221
(0.222)
0.708
(1.00)
0.391
(1.00)
1
(1.00)
1
(1.00)
2p loss 10 (2%) 489 0.639
(1.00)
0.29
(0.91)
0.0253
(0.24)
0.679
(1.00)
0.00733
(0.154)
1
(1.00)
0.732
(1.00)
1
(1.00)
0.00505
(0.15)
1
(1.00)
0.148
(0.652)
0.452
(1.00)
0.00366
(0.126)
1
(1.00)
0.997
(1.00)
1
(1.00)
1
(1.00)
2q loss 10 (2%) 489 0.619
(1.00)
0.264
(0.864)
0.0251
(0.24)
0.797
(1.00)
0.0149
(0.192)
1
(1.00)
0.732
(1.00)
0.495
(1.00)
0.00486
(0.15)
1
(1.00)
0.149
(0.653)
0.452
(1.00)
0.00663
(0.151)
1
(1.00)
0.349
(0.969)
1
(1.00)
1
(1.00)
3p gain 3 (1%) 496 0.0012
(0.0925)
0.0153
(0.192)
0.0333
(0.276)
0.0977
(0.497)
1
(1.00)
0.0314
(0.267)
0.568
(1.00)
0.297
(0.917)
0.222
(0.794)
1
(1.00)
0.611
(1.00)
0.0233
(0.232)
1
(1.00)
0.537
(1.00)
1
(1.00)
12p gain 15 (3%) 484 0.496
(1.00)
0.184
(0.707)
0.118
(0.578)
0.885
(1.00)
0.00176
(0.0983)
1
(1.00)
0.769
(1.00)
0.566
(1.00)
0.00583
(0.151)
1
(1.00)
0.178
(0.701)
0.545
(1.00)
0.00112
(0.0925)
1
(1.00)
0.94
(1.00)
0.8
(1.00)
1
(1.00)
12q gain 15 (3%) 484 0.496
(1.00)
0.184
(0.707)
0.12
(0.581)
0.882
(1.00)
0.00176
(0.0983)
1
(1.00)
0.769
(1.00)
0.566
(1.00)
0.00569
(0.151)
1
(1.00)
0.177
(0.7)
0.548
(1.00)
0.00112
(0.0925)
1
(1.00)
0.94
(1.00)
0.798
(1.00)
1
(1.00)
16p gain 15 (3%) 484 0.341
(0.958)
0.205
(0.763)
0.0344
(0.283)
0.904
(1.00)
0.0201
(0.215)
1
(1.00)
0.769
(1.00)
0.14
(0.631)
0.0825
(0.452)
1
(1.00)
0.0248
(0.24)
0.13
(0.603)
0.00202
(0.0983)
0.794
(1.00)
0.672
(1.00)
0.558
(1.00)
1
(1.00)
16q gain 13 (3%) 486 0.183
(0.707)
0.135
(0.614)
0.0197
(0.213)
0.723
(1.00)
0.0372
(0.301)
1
(1.00)
1
(1.00)
0.511
(1.00)
0.0457
(0.342)
1
(1.00)
0.0145
(0.192)
0.269
(0.869)
0.00366
(0.126)
1
(1.00)
0.609
(1.00)
0.778
(1.00)
1
(1.00)
13q loss 14 (3%) 485 0.326
(0.948)
0.0312
(0.267)
0.271
(0.87)
0.921
(1.00)
0.0108
(0.172)
1
(1.00)
0.54
(1.00)
0.775
(1.00)
0.431
(1.00)
0.000647
(0.0752)
0.495
(1.00)
0.671
(1.00)
0.0155
(0.192)
0.792
(1.00)
0.0933
(0.485)
0.709
(1.00)
0.615
(1.00)
4p gain 5 (1%) 494 0.00897
(0.154)
0.03
(0.264)
0.181
(0.707)
0.71
(1.00)
0.0611
(0.386)
1
(1.00)
1
(1.00)
0.168
(0.693)
1
(1.00)
1
(1.00)
0.389
(1.00)
0.0221
(0.222)
0.185
(0.707)
0.238
(0.816)
1
(1.00)
1
(1.00)
4q gain 5 (1%) 494 0.00897
(0.154)
0.03
(0.264)
0.183
(0.707)
0.708
(1.00)
0.0611
(0.386)
1
(1.00)
1
(1.00)
0.167
(0.691)
1
(1.00)
1
(1.00)
0.387
(1.00)
0.0221
(0.222)
0.185
(0.707)
0.238
(0.816)
1
(1.00)
1
(1.00)
17p gain 16 (3%) 483 0.445
(1.00)
0.0835
(0.455)
0.00304
(0.126)
0.857
(1.00)
0.0361
(0.294)
1
(1.00)
1
(1.00)
0.585
(1.00)
0.0428
(0.325)
1
(1.00)
0.78
(1.00)
0.324
(0.948)
0.0173
(0.2)
1
(1.00)
0.507
(1.00)
1
(1.00)
0.608
(1.00)
19p gain 8 (2%) 491 0.708
(1.00)
0.0538
(0.38)
0.625
(1.00)
0.618
(1.00)
0.0302
(0.264)
0.22
(0.794)
0.266
(0.866)
0.00951
(0.154)
1
(1.00)
0.603
(1.00)
0.457
(1.00)
0.0121
(0.176)
0.151
(0.655)
0.15
(0.653)
1
(1.00)
1
(1.00)
6q loss 7 (1%) 492 0.00225
(0.0983)
0.0819
(0.451)
0.194
(0.734)
0.793
(1.00)
0.372
(1.00)
0.392
(1.00)
0.0888
(0.471)
0.815
(1.00)
0.213
(0.782)
0.398
(1.00)
0.759
(1.00)
0.174
(0.694)
0.46
(1.00)
0.00914
(0.154)
1
(1.00)
1
(1.00)
9q loss 25 (5%) 474 0.0582
(0.386)
0.000853
(0.0855)
0.00051
(0.0731)
0.0974
(0.497)
0.513
(1.00)
0.277
(0.881)
0.353
(0.973)
1
(1.00)
1
(1.00)
1
(1.00)
0.0645
(0.401)
0.807
(1.00)
0.71
(1.00)
0.681
(1.00)
0.0529
(0.379)
0.501
(1.00)
1
(1.00)
10p loss 7 (1%) 492 0.649
(1.00)
0.337
(0.953)
0.114
(0.57)
0.283
(0.895)
0.0302
(0.264)
1
(1.00)
0.392
(1.00)
0.419
(1.00)
0.373
(1.00)
1
(1.00)
0.759
(1.00)
1
(1.00)
0.0221
(0.222)
0.708
(1.00)
0.0113
(0.176)
0.665
(1.00)
1
(1.00)
19p loss 5 (1%) 494 0.0858
(0.46)
0.501
(1.00)
0.231
(0.814)
1
(1.00)
1
(1.00)
1
(1.00)
0.614
(1.00)
1
(1.00)
1
(1.00)
0.0133
(0.19)
1
(1.00)
0.634
(1.00)
0.38
(1.00)
0.00914
(0.154)
1
(1.00)
1
(1.00)
1p gain 4 (1%) 495 0.756
(1.00)
0.164
(0.685)
0.00802
(0.154)
0.265
(0.865)
0.372
(1.00)
1
(1.00)
1
(1.00)
1
(1.00)
0.326
(0.948)
0.112
(0.565)
0.211
(0.776)
0.313
(0.94)
0.962
(1.00)
0.628
(1.00)
0.667
(1.00)
0.318
(0.942)
1
(1.00)
8q gain 7 (1%) 492 0.133
(0.611)
0.351
(0.969)
0.0545
(0.382)
0.396
(1.00)
1
(1.00)
1
(1.00)
0.681
(1.00)
0.655
(1.00)
0.815
(1.00)
1
(1.00)
0.00748
(0.154)
0.387
(1.00)
0.174
(0.694)
0.131
(0.604)
0.221
(0.794)
0.732
(1.00)
1
(1.00)
9q gain 4 (1%) 495 0.713
(1.00)
0.0328
(0.274)
0.0392
(0.31)
0.633
(1.00)
0.623
(1.00)
1
(1.00)
0.293
(0.916)
1
(1.00)
0.454
(1.00)
1
(1.00)
1
(1.00)
1
(1.00)
0.236
(0.816)
0.338
(0.953)
0.0253
(0.24)
1
(1.00)
1
(1.00)
14q gain 11 (2%) 488 0.572
(1.00)
0.0377
(0.303)
0.00649
(0.151)
0.379
(1.00)
0.0679
(0.405)
1
(1.00)
0.303
(0.926)
0.163
(0.685)
0.0577
(0.386)
1
(1.00)
0.831
(1.00)
0.492
(1.00)
0.0552
(0.385)
0.123
(0.581)
0.263
(0.864)
0.754
(1.00)
1
(1.00)
17q gain 18 (4%) 481 0.4
(1.00)
0.107
(0.544)
0.00819
(0.154)
0.486
(1.00)
0.0536
(0.38)
1
(1.00)
1
(1.00)
0.794
(1.00)
0.0773
(0.438)
1
(1.00)
0.405
(1.00)
0.56
(1.00)
0.0319
(0.269)
0.634
(1.00)
0.555
(1.00)
1
(1.00)
0.61
(1.00)
9p loss 19 (4%) 480 0.532
(1.00)
0.0974
(0.497)
0.0259
(0.24)
0.473
(1.00)
1
(1.00)
0.202
(0.758)
0.303
(0.926)
0.614
(1.00)
0.744
(1.00)
1
(1.00)
0.9
(1.00)
0.56
(1.00)
0.321
(0.948)
0.486
(1.00)
0.113
(0.565)
1
(1.00)
0.379
(1.00)
10q loss 6 (1%) 493 0.696
(1.00)
0.313
(0.94)
0.255
(0.845)
0.334
(0.952)
0.0611
(0.386)
1
(1.00)
0.35
(0.969)
0.655
(1.00)
0.778
(1.00)
1
(1.00)
0.748
(1.00)
1
(1.00)
0.041
(0.314)
0.421
(1.00)
0.00819
(0.154)
0.664
(1.00)
1
(1.00)
17p loss 8 (2%) 491 0.575
(1.00)
0.901
(1.00)
0.144
(0.643)
0.0309
(0.267)
0.724
(1.00)
1
(1.00)
1
(1.00)
0.478
(1.00)
0.225
(0.794)
0.274
(0.875)
0.0598
(0.386)
0.336
(0.953)
0.909
(1.00)
0.731
(1.00)
0.0141
(0.192)
0.584
(1.00)
1
(1.00)
21q loss 8 (2%) 491 0.74
(1.00)
0.121
(0.581)
0.0118
(0.176)
0.173
(0.694)
0.724
(1.00)
1
(1.00)
0.448
(1.00)
0.715
(1.00)
0.85
(1.00)
1
(1.00)
0.174
(0.694)
1
(1.00)
0.624
(1.00)
0.151
(0.655)
0.502
(1.00)
0.234
(0.816)
1
(1.00)
xp loss 4 (1%) 495 0.78
(1.00)
0.958
(1.00)
0.0237
(0.234)
0.308
(0.933)
0.623
(1.00)
0.293
(0.916)
0.302
(0.926)
1
(1.00)
1
(1.00)
0.647
(1.00)
1
(1.00)
0.49
(1.00)
1
(1.00)
1
(1.00)
xq loss 5 (1%) 494 0.742
(1.00)
0.598
(1.00)
0.00524
(0.15)
0.157
(0.668)
0.372
(1.00)
0.123
(0.581)
0.163
(0.685)
1
(1.00)
0.147
(0.652)
0.449
(1.00)
0.387
(1.00)
0.282
(0.894)
0.665
(1.00)
0.656
(1.00)
1
(1.00)
8p gain 6 (1%) 493 0.614
(1.00)
0.657
(1.00)
0.709
(1.00)
0.836
(1.00)
0.623
(1.00)
1
(1.00)
1
(1.00)
0.655
(1.00)
0.775
(1.00)
1
(1.00)
0.366
(0.993)
0.46
(1.00)
0.174
(0.694)
0.225
(0.794)
0.333
(0.952)
0.665
(1.00)
1
(1.00)
9p gain 3 (1%) 496 0.746
(1.00)
0.0799
(0.443)
0.0463
(0.343)
0.698
(1.00)
0.248
(0.83)
1
(1.00)
1
(1.00)
1
(1.00)
0.221
(0.794)
1
(1.00)
1
(1.00)
1
(1.00)
0.597
(1.00)
0.0603
(0.386)
1
(1.00)
11p gain 6 (1%) 493 0.575
(1.00)
0.753
(1.00)
0.71
(1.00)
0.766
(1.00)
0.123
(0.581)
1
(1.00)
0.35
(0.969)
1
(1.00)
0.232
(0.815)
1
(1.00)
0.365
(0.993)
0.459
(1.00)
0.0773
(0.438)
0.225
(0.794)
0.615
(1.00)
1
(1.00)
1
(1.00)
11q gain 5 (1%) 494 0.579
(1.00)
0.742
(1.00)
0.794
(1.00)
0.892
(1.00)
0.248
(0.83)
1
(1.00)
0.614
(1.00)
1
(1.00)
0.556
(1.00)
1
(1.00)
0.45
(1.00)
0.392
(1.00)
0.0652
(0.401)
0.975
(1.00)
1
(1.00)
1
(1.00)
13q gain 5 (1%) 494 0.752
(1.00)
0.156
(0.667)
0.0583
(0.386)
0.637
(1.00)
0.123
(0.581)
1
(1.00)
1
(1.00)
1
(1.00)
0.166
(0.691)
1
(1.00)
1
(1.00)
1
(1.00)
0.041
(0.314)
0.665
(1.00)
0.679
(1.00)
1
(1.00)
18p gain 6 (1%) 493 0.626
(1.00)
0.725
(1.00)
0.709
(1.00)
0.764
(1.00)
0.0611
(0.386)
1
(1.00)
0.662
(1.00)
1
(1.00)
1
(1.00)
1
(1.00)
1
(1.00)
0.391
(1.00)
0.041
(0.314)
0.692
(1.00)
0.802
(1.00)
1
(1.00)
1
(1.00)
18q gain 6 (1%) 493 0.626
(1.00)
0.725
(1.00)
0.705
(1.00)
0.763
(1.00)
0.0611
(0.386)
1
(1.00)
0.662
(1.00)
1
(1.00)
1
(1.00)
1
(1.00)
1
(1.00)
0.391
(1.00)
0.041
(0.314)
0.692
(1.00)
0.802
(1.00)
1
(1.00)
1
(1.00)
21q gain 5 (1%) 494 0.631
(1.00)
0.316
(0.941)
0.578
(1.00)
0.567
(1.00)
0.248
(0.83)
1
(1.00)
0.614
(1.00)
0.366
(0.993)
1
(1.00)
1
(1.00)
0.641
(1.00)
0.314
(0.941)
0.0652
(0.401)
0.126
(0.592)
1
(1.00)
1
(1.00)
1p loss 4 (1%) 495 0.67
(1.00)
0.549
(1.00)
0.134
(0.614)
0.635
(1.00)
0.248
(0.83)
1
(1.00)
0.578
(1.00)
1
(1.00)
0.45
(1.00)
1
(1.00)
0.644
(1.00)
1
(1.00)
0.628
(1.00)
0.117
(0.577)
0.478
(1.00)
1
(1.00)
1q loss 3 (1%) 496 0.681
(1.00)
0.822
(1.00)
0.329
(0.948)
0.806
(1.00)
0.499
(1.00)
0.568
(1.00)
0.531
(1.00)
0.222
(0.794)
1
(1.00)
0.61
(1.00)
1
(1.00)
1
(1.00)
0.117
(0.577)
1
(1.00)
3p loss 3 (1%) 496 0.725
(1.00)
0.574
(1.00)
0.333
(0.952)
0.808
(1.00)
0.499
(1.00)
1
(1.00)
0.531
(1.00)
0.638
(1.00)
1
(1.00)
0.609
(1.00)
1
(1.00)
0.597
(1.00)
0.0782
(0.439)
1
(1.00)
1
(1.00)
3q loss 4 (1%) 495 0.673
(1.00)
0.603
(1.00)
0.136
(0.615)
0.634
(1.00)
0.248
(0.83)
1
(1.00)
0.297
(0.917)
0.451
(1.00)
1
(1.00)
0.643
(1.00)
1
(1.00)
0.0773
(0.438)
1
(1.00)
0.0948
(0.49)
1
(1.00)
1
(1.00)
6p loss 4 (1%) 495 0.649
(1.00)
0.324
(0.948)
0.733
(1.00)
1
(1.00)
1
(1.00)
1
(1.00)
0.297
(0.917)
1
(1.00)
1
(1.00)
0.642
(1.00)
0.554
(1.00)
1
(1.00)
0.0576
(0.386)
1
(1.00)
1
(1.00)
8p loss 4 (1%) 495 0.82
(1.00)
0.913
(1.00)
0.17
(0.694)
0.871
(1.00)
0.248
(0.83)
1
(1.00)
0.0611
(0.386)
0.631
(1.00)
0.448
(1.00)
1
(1.00)
0.645
(1.00)
1
(1.00)
0.0773
(0.438)
1
(1.00)
0.737
(1.00)
1
(1.00)
8q loss 4 (1%) 495 0.82
(1.00)
0.913
(1.00)
0.174
(0.694)
0.872
(1.00)
0.248
(0.83)
1
(1.00)
0.0611
(0.386)
0.631
(1.00)
0.451
(1.00)
1
(1.00)
0.646
(1.00)
1
(1.00)
0.0773
(0.438)
1
(1.00)
0.737
(1.00)
1
(1.00)
15q loss 8 (2%) 491 0.574
(1.00)
0.754
(1.00)
0.238
(0.816)
0.731
(1.00)
0.122
(0.581)
0.0915
(0.478)
0.688
(1.00)
1
(1.00)
0.0451
(0.34)
1
(1.00)
0.601
(1.00)
0.784
(1.00)
0.135
(0.614)
0.731
(1.00)
0.0758
(0.438)
0.664
(1.00)
0.396
(1.00)
17q loss 4 (1%) 495 0.778
(1.00)
0.462
(1.00)
0.47
(1.00)
0.635
(1.00)
0.123
(0.581)
1
(1.00)
1
(1.00)
0.148
(0.652)
0.451
(1.00)
1
(1.00)
1
(1.00)
1
(1.00)
0.0773
(0.438)
1
(1.00)
0.398
(1.00)
1
(1.00)
18p loss 4 (1%) 495 0.676
(1.00)
0.672
(1.00)
0.172
(0.694)
0.308
(0.933)
1
(1.00)
1
(1.00)
1
(1.00)
0.631
(1.00)
0.448
(1.00)
1
(1.00)
0.645
(1.00)
1
(1.00)
0.328
(0.948)
0.628
(1.00)
0.647
(1.00)
0.182
(0.707)
18q loss 4 (1%) 495 0.676
(1.00)
0.672
(1.00)
0.173
(0.694)
0.307
(0.933)
1
(1.00)
1
(1.00)
1
(1.00)
0.631
(1.00)
0.452
(1.00)
1
(1.00)
0.643
(1.00)
1
(1.00)
0.328
(0.948)
0.628
(1.00)
0.647
(1.00)
0.182
(0.707)
22q loss 89 (18%) 410 0.238
(0.816)
0.458
(1.00)
0.68
(1.00)
0.861
(1.00)
0.326
(0.948)
0.644
(1.00)
0.43
(1.00)
0.0673
(0.405)
0.164
(0.685)
0.332
(0.952)
0.553
(1.00)
0.294
(0.917)
0.513
(1.00)
0.286
(0.901)
0.579
(1.00)
0.433
(1.00)
1
(1.00)
'1p gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00802 (Fisher's exact test), Q value = 0.15

Table S1.  Gene #1: '1p gain' 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
1P GAIN MUTATED 0 0 1 0 3 0
1P GAIN WILD-TYPE 282 50 110 2 43 6

Figure S1.  Get High-res Image Gene #1: '1p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'1q gain' versus 'YEARS_TO_BIRTH'

P value = 3.58e-05 (Wilcoxon-test), Q value = 0.012

Table S2.  Gene #2: '1q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 499 47.3 (15.8)
1Q GAIN MUTATED 26 60.5 (15.3)
1Q GAIN WILD-TYPE 473 46.5 (15.5)

Figure S2.  Get High-res Image Gene #2: '1q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'1q gain' versus 'PATHOLOGIC_STAGE'

P value = 3e-05 (Fisher's exact test), Q value = 0.012

Table S3.  Gene #2: '1q gain' 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
1Q GAIN MUTATED 6 0 11 1 8 0
1Q GAIN WILD-TYPE 276 50 100 1 38 6

Figure S3.  Get High-res Image Gene #2: '1q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'1q gain' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.01

Table S4.  Gene #2: '1q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 142 165 167 23
1Q GAIN MUTATED 2 3 16 5
1Q GAIN WILD-TYPE 140 162 151 18

Figure S4.  Get High-res Image Gene #2: '1q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'1q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00186 (Fisher's exact test), Q value = 0.098

Table S5.  Gene #2: '1q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 225 224
1Q GAIN MUTATED 5 20
1Q GAIN WILD-TYPE 220 204

Figure S5.  Get High-res Image Gene #2: '1q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'1q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0169 (Fisher's exact test), Q value = 0.2

Table S6.  Gene #2: '1q gain' 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
1Q GAIN MUTATED 0 23 0 3
1Q GAIN WILD-TYPE 7 333 100 33

Figure S6.  Get High-res Image Gene #2: '1q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'1q gain' versus 'EXTRATHYROIDAL_EXTENSION'

P value = 5e-05 (Fisher's exact test), Q value = 0.013

Table S7.  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 12 4 9 1
1Q GAIN WILD-TYPE 120 14 321 0

Figure S7.  Get High-res Image Gene #2: '1q gain' versus Clinical Feature #11: 'EXTRATHYROIDAL_EXTENSION'

'1q gain' versus 'TUMOR_SIZE'

P value = 0.00846 (Wilcoxon-test), Q value = 0.15

Table S8.  Gene #2: '1q gain' versus Clinical Feature #15: 'TUMOR_SIZE'

nPatients Mean (Std.Dev)
ALL 401 3.0 (1.6)
1Q GAIN MUTATED 21 3.8 (1.5)
1Q GAIN WILD-TYPE 380 2.9 (1.6)

Figure S8.  Get High-res Image Gene #2: '1q gain' versus Clinical Feature #15: 'TUMOR_SIZE'

'1q gain' versus 'RACE'

P value = 0.00206 (Fisher's exact test), Q value = 0.098

Table S9.  Gene #2: '1q gain' versus Clinical Feature #16: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 52 27 329
1Q GAIN MUTATED 1 1 5 18
1Q GAIN WILD-TYPE 0 51 22 311

Figure S9.  Get High-res Image Gene #2: '1q gain' versus Clinical Feature #16: 'RACE'

'3p gain' versus 'Time to Death'

P value = 0.0012 (logrank test), Q value = 0.092

Table S10.  Gene #3: '3p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 498 16 0.2 - 178.3 (31.2)
3P GAIN MUTATED 3 1 6.0 - 57.6 (10.7)
3P GAIN WILD-TYPE 495 15 0.2 - 178.3 (31.3)

Figure S10.  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 = 0.19

Table S11.  Gene #3: '3p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 499 47.3 (15.8)
3P GAIN MUTATED 3 70.3 (5.9)
3P GAIN WILD-TYPE 496 47.1 (15.7)

Figure S11.  Get High-res Image Gene #3: '3p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'3p gain' versus 'RESIDUAL_TUMOR'

P value = 0.0233 (Fisher's exact test), Q value = 0.23

Table S12.  Gene #3: '3p gain' versus Clinical Feature #12: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 383 51 4 30
3P GAIN MUTATED 1 0 0 2
3P GAIN WILD-TYPE 382 51 4 28

Figure S12.  Get High-res Image Gene #3: '3p gain' versus Clinical Feature #12: 'RESIDUAL_TUMOR'

'4p gain' versus 'Time to Death'

P value = 0.00897 (logrank test), Q value = 0.15

Table S13.  Gene #4: '4p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 498 16 0.2 - 178.3 (31.2)
4P GAIN MUTATED 5 1 7.8 - 57.0 (29.1)
4P GAIN WILD-TYPE 493 15 0.2 - 178.3 (31.3)

Figure S13.  Get High-res Image Gene #4: '4p gain' versus Clinical Feature #1: 'Time to Death'

'4p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0221 (Wilcoxon-test), Q value = 0.22

Table S14.  Gene #4: '4p gain' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 386 3.6 (6.0)
4P GAIN MUTATED 5 0.0 (0.0)
4P GAIN WILD-TYPE 381 3.6 (6.0)

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

'4q gain' versus 'Time to Death'

P value = 0.00897 (logrank test), Q value = 0.15

Table S15.  Gene #5: '4q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 498 16 0.2 - 178.3 (31.2)
4Q GAIN MUTATED 5 1 7.8 - 57.0 (29.1)
4Q GAIN WILD-TYPE 493 15 0.2 - 178.3 (31.3)

Figure S15.  Get High-res Image Gene #5: '4q gain' versus Clinical Feature #1: 'Time to Death'

'4q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0221 (Wilcoxon-test), Q value = 0.22

Table S16.  Gene #5: '4q gain' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 386 3.6 (6.0)
4Q GAIN MUTATED 5 0.0 (0.0)
4Q GAIN WILD-TYPE 381 3.6 (6.0)

Figure S16.  Get High-res Image Gene #5: '4q gain' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'5p gain' versus 'YEARS_TO_BIRTH'

P value = 0.000172 (Wilcoxon-test), Q value = 0.034

Table S17.  Gene #6: '5p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 499 47.3 (15.8)
5P GAIN MUTATED 21 60.7 (15.1)
5P GAIN WILD-TYPE 478 46.7 (15.5)

Figure S17.  Get High-res Image Gene #6: '5p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'5p gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00363 (Fisher's exact test), Q value = 0.13

Table S18.  Gene #6: '5p gain' 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
5P GAIN MUTATED 5 5 8 1 2 0
5P GAIN WILD-TYPE 277 45 103 1 44 6

Figure S18.  Get High-res Image Gene #6: '5p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'5p gain' versus 'EXTRATHYROIDAL_EXTENSION'

P value = 0.021 (Fisher's exact test), Q value = 0.22

Table S19.  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 S19.  Get High-res Image Gene #6: '5p gain' versus Clinical Feature #11: 'EXTRATHYROIDAL_EXTENSION'

'5p gain' versus 'TUMOR_SIZE'

P value = 0.0269 (Wilcoxon-test), Q value = 0.25

Table S20.  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 S20.  Get High-res Image Gene #6: '5p gain' versus Clinical Feature #15: 'TUMOR_SIZE'

'5q gain' versus 'Time to Death'

P value = 0.0154 (logrank test), Q value = 0.19

Table S21.  Gene #7: '5q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 498 16 0.2 - 178.3 (31.2)
5Q GAIN MUTATED 17 2 5.7 - 123.3 (23.9)
5Q GAIN WILD-TYPE 481 14 0.2 - 178.3 (31.3)

Figure S21.  Get High-res Image Gene #7: '5q gain' versus Clinical Feature #1: 'Time to Death'

'5q gain' versus 'YEARS_TO_BIRTH'

P value = 0.00787 (Wilcoxon-test), Q value = 0.15

Table S22.  Gene #7: '5q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 499 47.3 (15.8)
5Q GAIN MUTATED 17 57.4 (14.5)
5Q GAIN WILD-TYPE 482 46.9 (15.7)

Figure S22.  Get High-res Image Gene #7: '5q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'5q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00913 (Fisher's exact test), Q value = 0.15

Table S23.  Gene #7: '5q gain' 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
5Q GAIN MUTATED 5 5 5 1 1 0
5Q GAIN WILD-TYPE 277 45 106 1 45 6

Figure S23.  Get High-res Image Gene #7: '5q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'5q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0206 (Fisher's exact test), Q value = 0.22

Table S24.  Gene #7: '5q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 225 224
5Q GAIN MUTATED 11 2
5Q GAIN WILD-TYPE 214 222

Figure S24.  Get High-res Image Gene #7: '5q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'5q gain' versus 'EXTRATHYROIDAL_EXTENSION'

P value = 0.0176 (Fisher's exact test), Q value = 0.2

Table S25.  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 S25.  Get High-res Image Gene #7: '5q gain' versus Clinical Feature #11: 'EXTRATHYROIDAL_EXTENSION'

'5q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00337 (Wilcoxon-test), Q value = 0.13

Table S26.  Gene #7: '5q gain' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 386 3.6 (6.0)
5Q GAIN MUTATED 12 0.6 (2.0)
5Q GAIN WILD-TYPE 374 3.7 (6.0)

Figure S26.  Get High-res Image Gene #7: '5q gain' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'7p gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00919 (Fisher's exact test), Q value = 0.15

Table S27.  Gene #8: '7p gain' 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
7P GAIN MUTATED 7 6 3 1 1 0
7P GAIN WILD-TYPE 275 44 108 1 45 6

Figure S27.  Get High-res Image Gene #8: '7p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'7p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0116 (Fisher's exact test), Q value = 0.18

Table S28.  Gene #8: '7p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 225 224
7P GAIN MUTATED 12 2
7P GAIN WILD-TYPE 213 222

Figure S28.  Get High-res Image Gene #8: '7p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'7p gain' versus 'EXTRATHYROIDAL_EXTENSION'

P value = 0.00562 (Fisher's exact test), Q value = 0.15

Table S29.  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 S29.  Get High-res Image Gene #8: '7p gain' versus Clinical Feature #11: 'EXTRATHYROIDAL_EXTENSION'

'7p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00189 (Wilcoxon-test), Q value = 0.098

Table S30.  Gene #8: '7p gain' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 386 3.6 (6.0)
7P GAIN MUTATED 13 0.5 (1.9)
7P GAIN WILD-TYPE 373 3.7 (6.0)

Figure S30.  Get High-res Image Gene #8: '7p gain' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'7q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.0155 (Fisher's exact test), Q value = 0.19

Table S31.  Gene #9: '7q gain' 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
7Q GAIN MUTATED 8 6 4 1 1 0
7Q GAIN WILD-TYPE 274 44 107 1 45 6

Figure S31.  Get High-res Image Gene #9: '7q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'7q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0116 (Fisher's exact test), Q value = 0.18

Table S32.  Gene #9: '7q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 225 224
7Q GAIN MUTATED 12 2
7Q GAIN WILD-TYPE 213 222

Figure S32.  Get High-res Image Gene #9: '7q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'7q gain' versus 'HISTOLOGICAL_TYPE'

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

Table S33.  Gene #9: '7q gain' 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
7Q GAIN MUTATED 0 10 10 0
7Q GAIN WILD-TYPE 7 346 90 36

Figure S33.  Get High-res Image Gene #9: '7q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'7q gain' versus 'EXTRATHYROIDAL_EXTENSION'

P value = 0.0181 (Fisher's exact test), Q value = 0.2

Table S34.  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 S34.  Get High-res Image Gene #9: '7q gain' versus Clinical Feature #11: 'EXTRATHYROIDAL_EXTENSION'

'7q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00189 (Wilcoxon-test), Q value = 0.098

Table S35.  Gene #9: '7q gain' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 386 3.6 (6.0)
7Q GAIN MUTATED 13 0.5 (1.9)
7Q GAIN WILD-TYPE 373 3.7 (6.0)

Figure S35.  Get High-res Image Gene #9: '7q gain' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'8q gain' versus 'EXTRATHYROIDAL_EXTENSION'

P value = 0.00748 (Fisher's exact test), Q value = 0.15

Table S36.  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 S36.  Get High-res Image Gene #11: '8q gain' versus Clinical Feature #11: 'EXTRATHYROIDAL_EXTENSION'

'9q gain' versus 'TUMOR_SIZE'

P value = 0.0253 (Wilcoxon-test), Q value = 0.24

Table S37.  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 S37.  Get High-res Image Gene #13: '9q gain' versus Clinical Feature #15: 'TUMOR_SIZE'

'12p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00176 (Fisher's exact test), Q value = 0.098

Table S38.  Gene #16: '12p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 225 224
12P GAIN MUTATED 10 0
12P GAIN WILD-TYPE 215 224

Figure S38.  Get High-res Image Gene #16: '12p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'12p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00583 (Fisher's exact test), Q value = 0.15

Table S39.  Gene #16: '12p gain' 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
12P GAIN MUTATED 0 6 9 0
12P GAIN WILD-TYPE 7 350 91 36

Figure S39.  Get High-res Image Gene #16: '12p gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'12p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00112 (Wilcoxon-test), Q value = 0.092

Table S40.  Gene #16: '12p gain' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 386 3.6 (6.0)
12P GAIN MUTATED 10 0.0 (0.0)
12P GAIN WILD-TYPE 376 3.7 (6.0)

Figure S40.  Get High-res Image Gene #16: '12p gain' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'12q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00176 (Fisher's exact test), Q value = 0.098

Table S41.  Gene #17: '12q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 225 224
12Q GAIN MUTATED 10 0
12Q GAIN WILD-TYPE 215 224

Figure S41.  Get High-res Image Gene #17: '12q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'12q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00569 (Fisher's exact test), Q value = 0.15

Table S42.  Gene #17: '12q gain' 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
12Q GAIN MUTATED 0 6 9 0
12Q GAIN WILD-TYPE 7 350 91 36

Figure S42.  Get High-res Image Gene #17: '12q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'12q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00112 (Wilcoxon-test), Q value = 0.092

Table S43.  Gene #17: '12q gain' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 386 3.6 (6.0)
12Q GAIN MUTATED 10 0.0 (0.0)
12Q GAIN WILD-TYPE 376 3.7 (6.0)

Figure S43.  Get High-res Image Gene #17: '12q gain' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'14q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00649 (Fisher's exact test), Q value = 0.15

Table S44.  Gene #19: '14q gain' 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
14Q GAIN MUTATED 2 5 4 0 0 0
14Q GAIN WILD-TYPE 280 45 107 2 46 6

Figure S44.  Get High-res Image Gene #19: '14q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'16p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0201 (Fisher's exact test), Q value = 0.21

Table S45.  Gene #20: '16p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 225 224
16P GAIN MUTATED 9 1
16P GAIN WILD-TYPE 216 223

Figure S45.  Get High-res Image Gene #20: '16p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'16p gain' versus 'EXTRATHYROIDAL_EXTENSION'

P value = 0.0248 (Fisher's exact test), Q value = 0.24

Table S46.  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 S46.  Get High-res Image Gene #20: '16p gain' versus Clinical Feature #11: 'EXTRATHYROIDAL_EXTENSION'

'16p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00202 (Wilcoxon-test), Q value = 0.098

Table S47.  Gene #20: '16p gain' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 386 3.6 (6.0)
16P GAIN MUTATED 9 0.0 (0.0)
16P GAIN WILD-TYPE 377 3.7 (6.0)

Figure S47.  Get High-res Image Gene #20: '16p gain' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'16q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.0197 (Fisher's exact test), Q value = 0.21

Table S48.  Gene #21: '16q gain' 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
16Q GAIN MUTATED 6 4 2 1 0 0
16Q GAIN WILD-TYPE 276 46 109 1 46 6

Figure S48.  Get High-res Image Gene #21: '16q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'16q gain' versus 'EXTRATHYROIDAL_EXTENSION'

P value = 0.0145 (Fisher's exact test), Q value = 0.19

Table S49.  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 S49.  Get High-res Image Gene #21: '16q gain' versus Clinical Feature #11: 'EXTRATHYROIDAL_EXTENSION'

'16q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00366 (Wilcoxon-test), Q value = 0.13

Table S50.  Gene #21: '16q gain' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 386 3.6 (6.0)
16Q GAIN MUTATED 8 0.0 (0.0)
16Q GAIN WILD-TYPE 378 3.6 (6.0)

Figure S50.  Get High-res Image Gene #21: '16q gain' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'17p gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00304 (Fisher's exact test), Q value = 0.13

Table S51.  Gene #22: '17p gain' 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
17P GAIN MUTATED 6 6 3 1 0 0
17P GAIN WILD-TYPE 276 44 108 1 46 6

Figure S51.  Get High-res Image Gene #22: '17p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'17p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0173 (Wilcoxon-test), Q value = 0.2

Table S52.  Gene #22: '17p gain' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 386 3.6 (6.0)
17P GAIN MUTATED 11 0.6 (1.4)
17P GAIN WILD-TYPE 375 3.7 (6.0)

Figure S52.  Get High-res Image Gene #22: '17p gain' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'17q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00819 (Fisher's exact test), Q value = 0.15

Table S53.  Gene #23: '17q gain' 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
17Q GAIN MUTATED 7 6 3 1 1 0
17Q GAIN WILD-TYPE 275 44 108 1 45 6

Figure S53.  Get High-res Image Gene #23: '17q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'19p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00951 (Fisher's exact test), Q value = 0.15

Table S54.  Gene #26: '19p gain' 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
19P GAIN MUTATED 0 2 6 0
19P GAIN WILD-TYPE 7 354 94 36

Figure S54.  Get High-res Image Gene #26: '19p gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'19p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0121 (Wilcoxon-test), Q value = 0.18

Table S55.  Gene #26: '19p gain' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 386 3.6 (6.0)
19P GAIN MUTATED 6 0.0 (0.0)
19P GAIN WILD-TYPE 380 3.6 (6.0)

Figure S55.  Get High-res Image Gene #26: '19p gain' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'19q gain' versus 'YEARS_TO_BIRTH'

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

Table S56.  Gene #27: '19q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 499 47.3 (15.8)
19Q GAIN MUTATED 10 59.8 (15.6)
19Q GAIN WILD-TYPE 489 47.0 (15.7)

Figure S56.  Get High-res Image Gene #27: '19q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'19q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0149 (Fisher's exact test), Q value = 0.19

Table S57.  Gene #27: '19q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 225 224
19Q GAIN MUTATED 7 0
19Q GAIN WILD-TYPE 218 224

Figure S57.  Get High-res Image Gene #27: '19q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'19q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00514 (Fisher's exact test), Q value = 0.15

Table S58.  Gene #27: '19q gain' 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
19Q GAIN MUTATED 0 3 7 0
19Q GAIN WILD-TYPE 7 353 93 36

Figure S58.  Get High-res Image Gene #27: '19q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'19q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00663 (Wilcoxon-test), Q value = 0.15

Table S59.  Gene #27: '19q gain' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 386 3.6 (6.0)
19Q GAIN MUTATED 7 0.0 (0.0)
19Q GAIN WILD-TYPE 379 3.6 (6.0)

Figure S59.  Get High-res Image Gene #27: '19q gain' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'20p gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00923 (Fisher's exact test), Q value = 0.15

Table S60.  Gene #28: '20p gain' 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
20P GAIN MUTATED 4 4 3 1 0 0
20P GAIN WILD-TYPE 278 46 108 1 46 6

Figure S60.  Get High-res Image Gene #28: '20p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'20p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0044 (Fisher's exact test), Q value = 0.15

Table S61.  Gene #28: '20p gain' 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
20P GAIN MUTATED 0 4 8 0
20P GAIN WILD-TYPE 7 352 92 36

Figure S61.  Get High-res Image Gene #28: '20p gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'20p gain' versus 'EXTRATHYROIDAL_EXTENSION'

P value = 0.0134 (Fisher's exact test), Q value = 0.19

Table S62.  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 S62.  Get High-res Image Gene #28: '20p gain' versus Clinical Feature #11: 'EXTRATHYROIDAL_EXTENSION'

'20p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00663 (Wilcoxon-test), Q value = 0.15

Table S63.  Gene #28: '20p gain' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 386 3.6 (6.0)
20P GAIN MUTATED 7 0.0 (0.0)
20P GAIN WILD-TYPE 379 3.6 (6.0)

Figure S63.  Get High-res Image Gene #28: '20p gain' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'20q gain' versus 'PATHOLOGIC_STAGE'

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

Table S64.  Gene #29: '20q gain' 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
20Q GAIN MUTATED 4 4 3 1 0 0
20Q GAIN WILD-TYPE 278 46 108 1 46 6

Figure S64.  Get High-res Image Gene #29: '20q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'20q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00457 (Fisher's exact test), Q value = 0.15

Table S65.  Gene #29: '20q gain' 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
20Q GAIN MUTATED 0 4 8 0
20Q GAIN WILD-TYPE 7 352 92 36

Figure S65.  Get High-res Image Gene #29: '20q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'20q gain' versus 'EXTRATHYROIDAL_EXTENSION'

P value = 0.0137 (Fisher's exact test), Q value = 0.19

Table S66.  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 S66.  Get High-res Image Gene #29: '20q gain' versus Clinical Feature #11: 'EXTRATHYROIDAL_EXTENSION'

'20q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00663 (Wilcoxon-test), Q value = 0.15

Table S67.  Gene #29: '20q gain' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 386 3.6 (6.0)
20Q GAIN MUTATED 7 0.0 (0.0)
20Q GAIN WILD-TYPE 379 3.6 (6.0)

Figure S67.  Get High-res Image Gene #29: '20q gain' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'xp gain' versus 'YEARS_TO_BIRTH'

P value = 0.0142 (Wilcoxon-test), Q value = 0.19

Table S68.  Gene #31: 'xp gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 499 47.3 (15.8)
XP GAIN MUTATED 8 60.0 (10.9)
XP GAIN WILD-TYPE 491 47.1 (15.7)

Figure S68.  Get High-res Image Gene #31: 'xp gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'xp gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00746 (Fisher's exact test), Q value = 0.15

Table S69.  Gene #31: 'xp gain' 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
XP GAIN MUTATED 2 3 2 1 0 0
XP GAIN WILD-TYPE 280 47 109 1 46 6

Figure S69.  Get High-res Image Gene #31: 'xp gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'xp gain' versus 'EXTRATHYROIDAL_EXTENSION'

P value = 0.0182 (Fisher's exact test), Q value = 0.2

Table S70.  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 S70.  Get High-res Image Gene #31: 'xp gain' versus Clinical Feature #11: 'EXTRATHYROIDAL_EXTENSION'

'xp gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0121 (Wilcoxon-test), Q value = 0.18

Table S71.  Gene #31: 'xp gain' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 386 3.6 (6.0)
XP GAIN MUTATED 6 0.0 (0.0)
XP GAIN WILD-TYPE 380 3.6 (6.0)

Figure S71.  Get High-res Image Gene #31: 'xp gain' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'xq gain' versus 'YEARS_TO_BIRTH'

P value = 0.027 (Wilcoxon-test), Q value = 0.25

Table S72.  Gene #32: 'xq gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 499 47.3 (15.8)
XQ GAIN MUTATED 7 59.7 (11.8)
XQ GAIN WILD-TYPE 492 47.1 (15.7)

Figure S72.  Get High-res Image Gene #32: 'xq gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'xq gain' versus 'PATHOLOGIC_STAGE'

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

Table S73.  Gene #32: 'xq gain' 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
XQ GAIN MUTATED 2 2 2 1 0 0
XQ GAIN WILD-TYPE 280 48 109 1 46 6

Figure S73.  Get High-res Image Gene #32: 'xq gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'xq gain' versus 'EXTRATHYROIDAL_EXTENSION'

P value = 0.0186 (Fisher's exact test), Q value = 0.21

Table S74.  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 5 1
XQ GAIN WILD-TYPE 131 18 325 0

Figure S74.  Get High-res Image Gene #32: 'xq gain' versus Clinical Feature #11: 'EXTRATHYROIDAL_EXTENSION'

'xq gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0221 (Wilcoxon-test), Q value = 0.22

Table S75.  Gene #32: 'xq gain' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 386 3.6 (6.0)
XQ GAIN MUTATED 5 0.0 (0.0)
XQ GAIN WILD-TYPE 381 3.6 (6.0)

Figure S75.  Get High-res Image Gene #32: 'xq gain' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'2p loss' versus 'PATHOLOGIC_STAGE'

P value = 0.0253 (Fisher's exact test), Q value = 0.24

Table S76.  Gene #35: '2p loss' 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
2P LOSS MUTATED 4 5 1 0 0 0
2P LOSS WILD-TYPE 278 45 110 2 46 6

Figure S76.  Get High-res Image Gene #35: '2p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'2p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00733 (Fisher's exact test), Q value = 0.15

Table S77.  Gene #35: '2p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 225 224
2P LOSS MUTATED 8 0
2P LOSS WILD-TYPE 217 224

Figure S77.  Get High-res Image Gene #35: '2p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'2p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00505 (Fisher's exact test), Q value = 0.15

Table S78.  Gene #35: '2p loss' 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
2P LOSS MUTATED 0 3 7 0
2P LOSS WILD-TYPE 7 353 93 36

Figure S78.  Get High-res Image Gene #35: '2p loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'2p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00366 (Wilcoxon-test), Q value = 0.13

Table S79.  Gene #35: '2p loss' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 386 3.6 (6.0)
2P LOSS MUTATED 8 0.0 (0.0)
2P LOSS WILD-TYPE 378 3.6 (6.0)

Figure S79.  Get High-res Image Gene #35: '2p loss' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'2q loss' versus 'PATHOLOGIC_STAGE'

P value = 0.0251 (Fisher's exact test), Q value = 0.24

Table S80.  Gene #36: '2q loss' 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
2Q LOSS MUTATED 4 5 1 0 0 0
2Q LOSS WILD-TYPE 278 45 110 2 46 6

Figure S80.  Get High-res Image Gene #36: '2q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'2q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0149 (Fisher's exact test), Q value = 0.19

Table S81.  Gene #36: '2q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 225 224
2Q LOSS MUTATED 7 0
2Q LOSS WILD-TYPE 218 224

Figure S81.  Get High-res Image Gene #36: '2q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'2q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00486 (Fisher's exact test), Q value = 0.15

Table S82.  Gene #36: '2q loss' 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
2Q LOSS MUTATED 0 3 7 0
2Q LOSS WILD-TYPE 7 353 93 36

Figure S82.  Get High-res Image Gene #36: '2q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'2q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00663 (Wilcoxon-test), Q value = 0.15

Table S83.  Gene #36: '2q loss' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 386 3.6 (6.0)
2Q LOSS MUTATED 7 0.0 (0.0)
2Q LOSS WILD-TYPE 379 3.6 (6.0)

Figure S83.  Get High-res Image Gene #36: '2q loss' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'6q loss' versus 'Time to Death'

P value = 0.00225 (logrank test), Q value = 0.098

Table S84.  Gene #40: '6q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 498 16 0.2 - 178.3 (31.2)
6Q LOSS MUTATED 7 2 7.8 - 123.3 (33.6)
6Q LOSS WILD-TYPE 491 14 0.2 - 178.3 (31.1)

Figure S84.  Get High-res Image Gene #40: '6q loss' versus Clinical Feature #1: 'Time to Death'

'6q loss' versus 'TUMOR_SIZE'

P value = 0.00914 (Wilcoxon-test), Q value = 0.15

Table S85.  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 2.9 (1.6)

Figure S85.  Get High-res Image Gene #40: '6q loss' versus Clinical Feature #15: 'TUMOR_SIZE'

'9p loss' versus 'PATHOLOGIC_STAGE'

P value = 0.0259 (Fisher's exact test), Q value = 0.24

Table S86.  Gene #43: '9p loss' 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
9P LOSS MUTATED 8 4 4 1 1 1
9P LOSS WILD-TYPE 274 46 107 1 45 5

Figure S86.  Get High-res Image Gene #43: '9p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'9q loss' versus 'YEARS_TO_BIRTH'

P value = 0.000853 (Wilcoxon-test), Q value = 0.086

Table S87.  Gene #44: '9q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 499 47.3 (15.8)
9Q LOSS MUTATED 25 58.9 (18.2)
9Q LOSS WILD-TYPE 474 46.7 (15.4)

Figure S87.  Get High-res Image Gene #44: '9q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'9q loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00051 (Fisher's exact test), Q value = 0.073

Table S88.  Gene #44: '9q loss' 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
9Q LOSS MUTATED 9 5 4 2 4 1
9Q LOSS WILD-TYPE 273 45 107 0 42 5

Figure S88.  Get High-res Image Gene #44: '9q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'10p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0221 (Wilcoxon-test), Q value = 0.22

Table S89.  Gene #45: '10p loss' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 386 3.6 (6.0)
10P LOSS MUTATED 5 0.0 (0.0)
10P LOSS WILD-TYPE 381 3.6 (6.0)

Figure S89.  Get High-res Image Gene #45: '10p loss' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'10p loss' versus 'TUMOR_SIZE'

P value = 0.0113 (Wilcoxon-test), Q value = 0.18

Table S90.  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 2.9 (1.6)

Figure S90.  Get High-res Image Gene #45: '10p loss' versus Clinical Feature #15: 'TUMOR_SIZE'

'10q loss' versus 'TUMOR_SIZE'

P value = 0.00819 (Wilcoxon-test), Q value = 0.15

Table S91.  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 2.9 (1.6)

Figure S91.  Get High-res Image Gene #46: '10q loss' versus Clinical Feature #15: 'TUMOR_SIZE'

'11p loss' versus 'Time to Death'

P value = 0.0167 (logrank test), Q value = 0.2

Table S92.  Gene #47: '11p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 498 16 0.2 - 178.3 (31.2)
11P LOSS MUTATED 7 1 7.8 - 49.5 (23.9)
11P LOSS WILD-TYPE 491 15 0.2 - 178.3 (31.3)

Figure S92.  Get High-res Image Gene #47: '11p loss' versus Clinical Feature #1: 'Time to Death'

'11p loss' versus 'YEARS_TO_BIRTH'

P value = 0.000675 (Wilcoxon-test), Q value = 0.075

Table S93.  Gene #47: '11p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 499 47.3 (15.8)
11P LOSS MUTATED 7 68.1 (8.7)
11P LOSS WILD-TYPE 492 47.0 (15.6)

Figure S93.  Get High-res Image Gene #47: '11p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'11p loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00613 (Fisher's exact test), Q value = 0.15

Table S94.  Gene #47: '11p loss' 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
11P LOSS MUTATED 1 1 4 1 0 0
11P LOSS WILD-TYPE 281 49 107 1 46 6

Figure S94.  Get High-res Image Gene #47: '11p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'11p loss' versus 'GENDER'

P value = 0.017 (Fisher's exact test), Q value = 0.2

Table S95.  Gene #47: '11p loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 365 134
11P LOSS MUTATED 2 5
11P LOSS WILD-TYPE 363 129

Figure S95.  Get High-res Image Gene #47: '11p loss' versus Clinical Feature #7: 'GENDER'

'11p loss' versus 'TUMOR_SIZE'

P value = 0.00751 (Wilcoxon-test), Q value = 0.15

Table S96.  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 S96.  Get High-res Image Gene #47: '11p loss' versus Clinical Feature #15: 'TUMOR_SIZE'

'11q loss' versus 'Time to Death'

P value = 0.0258 (logrank test), Q value = 0.24

Table S97.  Gene #48: '11q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 498 16 0.2 - 178.3 (31.2)
11Q LOSS MUTATED 9 1 7.8 - 49.5 (23.9)
11Q LOSS WILD-TYPE 489 15 0.2 - 178.3 (31.3)

Figure S97.  Get High-res Image Gene #48: '11q loss' versus Clinical Feature #1: 'Time to Death'

'11q loss' versus 'YEARS_TO_BIRTH'

P value = 0.000203 (Wilcoxon-test), Q value = 0.034

Table S98.  Gene #48: '11q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 499 47.3 (15.8)
11Q LOSS MUTATED 9 67.0 (8.9)
11Q LOSS WILD-TYPE 490 46.9 (15.6)

Figure S98.  Get High-res Image Gene #48: '11q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'11q loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00349 (Fisher's exact test), Q value = 0.13

Table S99.  Gene #48: '11q loss' 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
11Q LOSS MUTATED 1 2 4 1 1 0
11Q LOSS WILD-TYPE 281 48 107 1 45 6

Figure S99.  Get High-res Image Gene #48: '11q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'11q loss' versus 'GENDER'

P value = 0.00193 (Fisher's exact test), Q value = 0.098

Table S100.  Gene #48: '11q loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 365 134
11Q LOSS MUTATED 2 7
11Q LOSS WILD-TYPE 363 127

Figure S100.  Get High-res Image Gene #48: '11q loss' versus Clinical Feature #7: 'GENDER'

'11q loss' versus 'TUMOR_SIZE'

P value = 0.00222 (Wilcoxon-test), Q value = 0.098

Table S101.  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 (1.5)

Figure S101.  Get High-res Image Gene #48: '11q loss' versus Clinical Feature #15: 'TUMOR_SIZE'

'13q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0108 (Fisher's exact test), Q value = 0.17

Table S102.  Gene #49: '13q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 225 224
13Q LOSS MUTATED 10 1
13Q LOSS WILD-TYPE 215 223

Figure S102.  Get High-res Image Gene #49: '13q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'13q loss' versus 'RADIATION_EXPOSURE'

P value = 0.000647 (Fisher's exact test), Q value = 0.075

Table S103.  Gene #49: '13q loss' versus Clinical Feature #10: 'RADIATION_EXPOSURE'

nPatients NO YES
ALL 420 17
13Q LOSS MUTATED 8 4
13Q LOSS WILD-TYPE 412 13

Figure S103.  Get High-res Image Gene #49: '13q loss' versus Clinical Feature #10: 'RADIATION_EXPOSURE'

'13q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0155 (Wilcoxon-test), Q value = 0.19

Table S104.  Gene #49: '13q loss' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 386 3.6 (6.0)
13Q LOSS MUTATED 8 0.2 (0.7)
13Q LOSS WILD-TYPE 378 3.6 (6.0)

Figure S104.  Get High-res Image Gene #49: '13q loss' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'17p loss' versus 'TUMOR_SIZE'

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

Table S105.  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 2.9 (1.6)

Figure S105.  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 = 0.19

Table S106.  Gene #55: '19p loss' versus Clinical Feature #10: 'RADIATION_EXPOSURE'

nPatients NO YES
ALL 420 17
19P LOSS MUTATED 3 2
19P LOSS WILD-TYPE 417 15

Figure S106.  Get High-res Image Gene #55: '19p loss' versus Clinical Feature #10: 'RADIATION_EXPOSURE'

'19p loss' versus 'TUMOR_SIZE'

P value = 0.00914 (Wilcoxon-test), Q value = 0.15

Table S107.  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 2.9 (1.6)

Figure S107.  Get High-res Image Gene #55: '19p loss' versus Clinical Feature #15: 'TUMOR_SIZE'

'21q loss' versus 'PATHOLOGIC_STAGE'

P value = 0.0118 (Fisher's exact test), Q value = 0.18

Table S108.  Gene #56: '21q loss' 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
21Q LOSS MUTATED 1 4 2 0 1 0
21Q LOSS WILD-TYPE 281 46 109 2 45 6

Figure S108.  Get High-res Image Gene #56: '21q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'xp loss' versus 'PATHOLOGIC_STAGE'

P value = 0.0237 (Fisher's exact test), Q value = 0.23

Table S109.  Gene #58: 'xp loss' 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
XP LOSS MUTATED 1 3 0 0 0 0
XP LOSS WILD-TYPE 281 47 111 2 46 6

Figure S109.  Get High-res Image Gene #58: 'xp loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'xq loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00524 (Fisher's exact test), Q value = 0.15

Table S110.  Gene #59: 'xq loss' 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
XQ LOSS MUTATED 1 4 0 0 0 0
XQ LOSS WILD-TYPE 281 46 111 2 46 6

Figure S110.  Get High-res Image Gene #59: 'xq loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

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/22511440/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 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)