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

Overview

Introduction

This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.

Summary

Testing the association between copy number variation 96 focal events and 17 clinical features across 499 patients, 158 significant findings detected with Q value < 0.25.

amp_1p36.32 cnv correlated to 'RACE'.
amp_1p32.3 cnv correlated to 'RADIATION_EXPOSURE'.
amp_1q31.2 cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'HISTOLOGICAL_TYPE', 'EXTRATHYROIDAL_EXTENSION', 'TUMOR_SIZE', and 'RACE'.
amp_1q43 cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'HISTOLOGICAL_TYPE', 'EXTRATHYROIDAL_EXTENSION', 'TUMOR_SIZE', and 'RACE'.
amp_3p22.3 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', and 'PATHOLOGIC_STAGE'.
amp_3p14.1 cnv correlated to 'Time to Death'.
amp_4p16.1 cnv correlated to 'Time to Death', 'PATHOLOGY_N_STAGE', and 'NUMBER_OF_LYMPH_NODES'.
amp_4q28.2 cnv correlated to 'Time to Death' and 'NUMBER_OF_LYMPH_NODES'.
amp_4q31.21 cnv correlated to 'NUMBER_OF_LYMPH_NODES'.
amp_4q32.3 cnv correlated to 'PATHOLOGY_N_STAGE' and 'NUMBER_OF_LYMPH_NODES'.
amp_5p14.3 cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', and 'TUMOR_SIZE'.
amp_5q21.1 cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_N_STAGE', and 'NUMBER_OF_LYMPH_NODES'.
amp_5q21.1 cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_N_STAGE', 'NUMBER_OF_LYMPH_NODES', and 'TUMOR_SIZE'.
amp_5q33.1 cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_N_STAGE', and 'NUMBER_OF_LYMPH_NODES'.
amp_5q35.2 cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_N_STAGE', 'HISTOLOGICAL_TYPE', 'EXTRATHYROIDAL_EXTENSION', 'NUMBER_OF_LYMPH_NODES', and 'TUMOR_SIZE'.
amp_6p22.3 cnv correlated to 'Time to Death'.
amp_6p22.2 cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.
amp_6p21.31 cnv correlated to 'Time to Death' and 'PATHOLOGIC_STAGE'.
amp_7q11.21 cnv correlated to 'PATHOLOGIC_STAGE', 'PATHOLOGY_N_STAGE', 'EXTRATHYROIDAL_EXTENSION', and 'NUMBER_OF_LYMPH_NODES'.
amp_7q21.11 cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_N_STAGE', 'EXTRATHYROIDAL_EXTENSION', and 'NUMBER_OF_LYMPH_NODES'.
amp_7q31.1 cnv correlated to 'HISTOLOGICAL_TYPE' and 'NUMBER_OF_LYMPH_NODES'.
amp_7q34 cnv correlated to 'PATHOLOGY_N_STAGE', 'HISTOLOGICAL_TYPE', 'EXTRATHYROIDAL_EXTENSION', and 'NUMBER_OF_LYMPH_NODES'.
amp_9q31.1 cnv correlated to 'TUMOR_SIZE'.
amp_9q34.3 cnv correlated to 'TUMOR_SIZE'.
amp_10q24.2 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', and 'HISTOLOGICAL_TYPE'.
amp_12p11.1 cnv correlated to 'PATHOLOGY_N_STAGE', 'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.
amp_12q21.31 cnv correlated to 'PATHOLOGY_N_STAGE', 'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.
amp_12q23.1 cnv correlated to 'PATHOLOGY_N_STAGE', 'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.
amp_13q34 cnv correlated to 'HISTOLOGICAL_TYPE'.
amp_14q12 cnv correlated to 'PATHOLOGIC_STAGE'.
amp_14q32.31 cnv correlated to 'PATHOLOGIC_STAGE', 'PATHOLOGY_N_STAGE', and 'NUMBER_OF_LYMPH_NODES'.
amp_18q22.3 cnv correlated to 'PATHOLOGY_N_STAGE' and 'NUMBER_OF_LYMPH_NODES'.
amp_19p13.3 cnv correlated to 'HISTOLOGICAL_TYPE'.
amp_20p13 cnv correlated to 'PATHOLOGIC_STAGE', 'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.
amp_20q13.11 cnv correlated to 'PATHOLOGY_N_STAGE', 'HISTOLOGICAL_TYPE', 'EXTRATHYROIDAL_EXTENSION', and 'NUMBER_OF_LYMPH_NODES'.
amp_20q13.2 cnv correlated to 'YEARS_TO_BIRTH', 'HISTOLOGICAL_TYPE', 'EXTRATHYROIDAL_EXTENSION', and 'NUMBER_OF_LYMPH_NODES'.
amp_20q13.2 cnv correlated to 'PATHOLOGIC_STAGE', 'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.
amp_22q11.21 cnv correlated to 'RESIDUAL_TUMOR'.
amp_xp22.12 cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', and 'RESIDUAL_TUMOR'.
amp_xp11.4 cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', and 'EXTRATHYROIDAL_EXTENSION'.
amp_xq21.2 cnv correlated to 'EXTRATHYROIDAL_EXTENSION'.
amp_xq22.3 cnv correlated to 'GENDER' and 'EXTRATHYROIDAL_EXTENSION'.
amp_xq23 cnv correlated to 'EXTRATHYROIDAL_EXTENSION'.
amp_xq28 cnv correlated to 'YEARS_TO_BIRTH' and 'EXTRATHYROIDAL_EXTENSION'.
del_2p23.1 cnv correlated to 'PATHOLOGY_N_STAGE', 'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.
del_2q22.1 cnv correlated to 'PATHOLOGY_N_STAGE', 'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.
del_2q37.3 cnv correlated to 'PATHOLOGIC_STAGE' and 'NUMBER_OF_LYMPH_NODES'.
del_6q22.31 cnv correlated to 'Time to Death' and 'TUMOR_SIZE'.
del_8q24.22 cnv correlated to 'GENDER'.
del_9p21.3 cnv correlated to 'YEARS_TO_BIRTH' and 'PATHOLOGIC_STAGE'.
del_9q22.33 cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', and 'TUMOR_SIZE'.
del_10p12.31 cnv correlated to 'NUMBER_OF_LYMPH_NODES'.
del_10q23.31 cnv correlated to 'PATHOLOGY_N_STAGE' and 'TUMOR_SIZE'.
del_11p15.1 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'GENDER', and 'TUMOR_SIZE'.
del_13q12.13 cnv correlated to 'YEARS_TO_BIRTH' and 'RADIATION_EXPOSURE'.
del_13q22.1 cnv correlated to 'PATHOLOGY_N_STAGE' and 'RADIATION_EXPOSURE'.
del_16q23.3 cnv correlated to 'PATHOLOGIC_STAGE' and 'PATHOLOGY_T_STAGE'.
del_17p13.1 cnv correlated to 'TUMOR_SIZE'.
del_19p13.2 cnv correlated to 'TUMOR_SIZE'.
del_19p13.12 cnv correlated to 'TUMOR_SIZE'.
del_21q21.1 cnv correlated to 'PATHOLOGIC_STAGE'.
del_xq23 cnv correlated to 'PATHOLOGIC_STAGE'.
del_xq22.3 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 96 focal events and 17 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 158 significant findings detected.


		Clinical Features	Time to Death	YEARS TO BIRTH	PATHOLOGIC STAGE	PATHOLOGY T STAGE	PATHOLOGY N STAGE	PATHOLOGY M STAGE	GENDER	RADIATION THERAPY	HISTOLOGICAL TYPE	RADIATION EXPOSURE	EXTRATHYROIDAL EXTENSION	RESIDUAL TUMOR	NUMBER OF LYMPH NODES	MULTIFOCALITY	TUMOR SIZE	RACE	ETHNICITY
	nCNV (%)	nWild-Type	logrank test	Wilcoxon-test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Wilcoxon-test	Fisher's exact test	Wilcoxon-test	Fisher's exact test	Fisher's exact test
amp 1q31 2	29 (6%)	470	0.18 (0.672)	5.12e-05 (0.0087)	1e-05 (0.00272)	1e-05 (0.00272)	0.000629 (0.06)	1 (1.00)	0.666 (1.00)	0.532 (1.00)	0.00636 (0.156)	1 (1.00)	3e-05 (0.00699)	0.0434 (0.33)	0.0281 (0.262)	0.124 (0.546)	0.00305 (0.116)	0.0034 (0.121)	0.0282 (0.262)
amp 1q43	29 (6%)	470	0.0325 (0.28)	2.73e-06 (0.00222)	1e-05 (0.00272)	1e-05 (0.00272)	0.00166 (0.112)	0.387 (0.962)	1 (1.00)	0.532 (1.00)	0.00594 (0.156)	1 (1.00)	5e-05 (0.0087)	0.0424 (0.324)	0.0469 (0.342)	0.0535 (0.356)	0.00531 (0.152)	0.00349 (0.121)	0.0899 (0.473)
amp 5q35 2	20 (4%)	479	0.0506 (0.345)	0.00287 (0.114)	0.0027 (0.113)	0.116 (0.541)	0.0191 (0.219)	1 (1.00)	0.199 (0.708)	0.46 (1.00)	0.0177 (0.218)	1 (1.00)	0.0118 (0.184)	0.503 (1.00)	0.00617 (0.156)	1 (1.00)	0.00728 (0.161)	0.44 (1.00)	0.615 (1.00)
amp 5q21 1	20 (4%)	479	0.0604 (0.378)	0.00197 (0.112)	0.00068 (0.06)	0.286 (0.839)	0.00358 (0.121)	1 (1.00)	0.199 (0.708)	0.46 (1.00)	0.0573 (0.371)	1 (1.00)	0.0277 (0.262)	0.506 (1.00)	0.00192 (0.112)	0.652 (1.00)	0.0116 (0.184)	0.44 (1.00)	1 (1.00)
amp 7q21 11	21 (4%)	478	0.448 (1.00)	0.0092 (0.175)	0.0223 (0.233)	0.456 (1.00)	0.0191 (0.219)	1 (1.00)	0.806 (1.00)	0.335 (0.879)	0.0246 (0.252)	1 (1.00)	0.0147 (0.201)	0.502 (1.00)	0.00108 (0.0798)	0.509 (1.00)	0.576 (1.00)	0.352 (0.905)	0.623 (1.00)
del 11p15 1	7 (1%)	492	0.0193 (0.219)	0.000675 (0.06)	0.0055 (0.155)	0.232 (0.763)	0.449 (1.00)	1 (1.00)	0.017 (0.214)	0.412 (0.981)	0.817 (1.00)	1 (1.00)	0.557 (1.00)	0.529 (1.00)	0.21 (0.737)	0.708 (1.00)	0.00751 (0.161)	0.473 (1.00)	1 (1.00)
amp 5q21 1	23 (5%)	476	0.0837 (0.458)	0.022 (0.233)	0.00763 (0.161)	0.706 (1.00)	0.0168 (0.214)	1 (1.00)	0.226 (0.757)	0.634 (1.00)	0.356 (0.911)	1 (1.00)	0.0488 (0.343)	0.407 (0.975)	0.00813 (0.167)	0.834 (1.00)	0.165 (0.654)	0.223 (0.754)	1 (1.00)
amp 5q33 1	21 (4%)	478	0.0368 (0.296)	0.0131 (0.191)	0.00379 (0.121)	0.555 (1.00)	0.0191 (0.219)	1 (1.00)	0.312 (0.86)	0.461 (1.00)	0.101 (0.497)	1 (1.00)	0.0288 (0.264)	0.394 (0.962)	0.0101 (0.175)	1 (1.00)	0.0825 (0.455)	1 (1.00)	0.623 (1.00)
amp 7q11 21	20 (4%)	479	0.402 (0.964)	0.0946 (0.481)	0.0178 (0.218)	0.517 (1.00)	0.00649 (0.156)	1 (1.00)	0.797 (1.00)	0.796 (1.00)	0.056 (0.371)	1 (1.00)	0.00432 (0.136)	0.477 (1.00)	0.00192 (0.112)	0.817 (1.00)	0.349 (0.904)	1 (1.00)	0.615 (1.00)
amp 7q34	22 (4%)	477	0.526 (1.00)	0.0594 (0.378)	0.0284 (0.262)	0.705 (1.00)	0.0191 (0.219)	1 (1.00)	0.808 (1.00)	0.477 (1.00)	0.0105 (0.175)	1 (1.00)	0.0119 (0.184)	0.323 (0.874)	0.00562 (0.155)	0.668 (1.00)	0.552 (1.00)	0.35 (0.904)	1 (1.00)
amp 20q13 11	14 (3%)	485	0.395 (0.962)	0.266 (0.807)	0.0249 (0.252)	0.481 (1.00)	0.0201 (0.222)	1 (1.00)	1 (1.00)	0.773 (1.00)	0.00358 (0.121)	1 (1.00)	0.0102 (0.175)	1 (1.00)	0.00206 (0.112)	1 (1.00)	0.122 (0.546)	0.758 (1.00)	0.173 (0.666)
amp 20q13 2	14 (3%)	485	0.324 (0.874)	0.0223 (0.233)	0.0247 (0.252)	0.709 (1.00)	0.105 (0.512)	1 (1.00)	0.218 (0.743)	0.773 (1.00)	0.00376 (0.121)	1 (1.00)	0.0097 (0.175)	1 (1.00)	0.0223 (0.233)	0.792 (1.00)	0.0752 (0.436)	0.779 (1.00)	1 (1.00)
amp 3p22 3	4 (1%)	495	0.00231 (0.112)	0.0151 (0.203)	0.0096 (0.175)	0.109 (0.526)	1 (1.00)	0.0314 (0.277)	1 (1.00)	0.16 (0.645)	0.454 (1.00)	1 (1.00)	0.644 (1.00)	0.0472 (0.342)	0.0778 (0.438)	0.628 (1.00)	0.537 (1.00)		1 (1.00)
amp 4p16 1	7 (1%)	492	0.0117 (0.184)	0.0459 (0.341)	0.19 (0.692)	0.737 (1.00)	0.0149 (0.201)	1 (1.00)	0.392 (0.962)	1 (1.00)	0.384 (0.959)	1 (1.00)	1 (1.00)	0.529 (1.00)	0.0122 (0.184)	0.256 (0.79)	0.236 (0.763)	0.586 (1.00)	1 (1.00)
amp 5p14 3	23 (5%)	476	0.0868 (0.466)	5.33e-05 (0.0087)	0.00141 (0.1)	0.15 (0.625)	0.64 (1.00)	1 (1.00)	0.639 (1.00)	0.244 (0.773)	0.355 (0.91)	1 (1.00)	0.032 (0.28)	0.0816 (0.453)	0.141 (0.599)	0.529 (1.00)	0.0162 (0.21)	0.299 (0.849)	0.645 (1.00)
amp 10q24 2	3 (1%)	496	0.00835 (0.168)	0.00952 (0.175)	1 (1.00)	0.39 (0.962)	0.499 (1.00)		0.568 (1.00)	0.523 (1.00)	0.0207 (0.225)	1 (1.00)	0.61 (1.00)	0.235 (0.763)		1 (1.00)			1 (1.00)
amp 12p11 1	16 (3%)	483	0.445 (1.00)	0.117 (0.541)	0.115 (0.539)	0.836 (1.00)	0.00176 (0.112)	1 (1.00)	0.576 (1.00)	0.786 (1.00)	0.0024 (0.112)	1 (1.00)	0.409 (0.978)	0.226 (0.757)	0.00206 (0.112)	1 (1.00)	0.81 (1.00)	0.555 (1.00)	1 (1.00)
amp 12q21 31	17 (3%)	482	0.421 (0.999)	0.176 (0.669)	0.0573 (0.371)	0.592 (1.00)	0.00042 (0.0571)	1 (1.00)	0.578 (1.00)	0.595 (1.00)	0.0183 (0.219)	1 (1.00)	0.114 (0.539)	0.595 (1.00)	0.000634 (0.06)	0.806 (1.00)	0.707 (1.00)	0.485 (1.00)	1 (1.00)
amp 12q23 1	17 (3%)	482	0.49 (1.00)	0.0857 (0.465)	0.0457 (0.341)	0.593 (1.00)	0.00572 (0.156)	1 (1.00)	0.578 (1.00)	0.595 (1.00)	0.0179 (0.218)	1 (1.00)	0.112 (0.535)	0.595 (1.00)	0.00611 (0.156)	0.625 (1.00)	0.907 (1.00)	0.487 (1.00)	1 (1.00)
amp 14q32 31	13 (3%)	486	0.559 (1.00)	0.0456 (0.341)	0.00312 (0.116)	0.307 (0.854)	0.0201 (0.222)	1 (1.00)	0.529 (1.00)	0.057 (0.371)	0.0305 (0.272)	1 (1.00)	0.862 (1.00)	0.558 (1.00)	0.0174 (0.217)	0.099 (0.492)	0.224 (0.754)	0.777 (1.00)	1 (1.00)
amp 20p13	14 (3%)	485	0.428 (1.00)	0.153 (0.632)	0.0145 (0.201)	0.505 (1.00)	0.0372 (0.296)	1 (1.00)	1 (1.00)	1 (1.00)	0.017 (0.214)	1 (1.00)	0.0325 (0.28)	0.453 (1.00)	0.00371 (0.121)	1 (1.00)	0.0369 (0.296)	0.78 (1.00)	0.508 (1.00)
amp 20q13 2	13 (3%)	486	0.276 (0.828)	0.0571 (0.371)	0.00735 (0.161)	0.483 (1.00)	0.175 (0.669)	1 (1.00)	0.755 (1.00)	0.541 (1.00)	0.00474 (0.143)	1 (1.00)	0.0376 (0.296)	0.649 (1.00)	0.0239 (0.247)	0.586 (1.00)	0.0466 (0.342)	0.546 (1.00)	1 (1.00)
amp xp22 12	10 (2%)	489	0.0956 (0.483)	0.0131 (0.191)	0.00252 (0.113)	0.301 (0.849)	0.175 (0.669)	1 (1.00)	1 (1.00)	0.492 (1.00)	0.449 (1.00)	0.303 (0.849)	0.0321 (0.28)	0.0153 (0.203)	0.0507 (0.345)	0.524 (1.00)	0.21 (0.737)	0.472 (1.00)	1 (1.00)
amp xp11 4	9 (2%)	490	0.0912 (0.473)	0.00502 (0.149)	0.00754 (0.161)	0.351 (0.905)	0.285 (0.838)	1 (1.00)	1 (1.00)	0.711 (1.00)	0.326 (0.874)	0.303 (0.849)	0.0192 (0.219)	0.084 (0.458)	0.0703 (0.416)	0.739 (1.00)	0.21 (0.737)	1 (1.00)	1 (1.00)
del 2p23 1	12 (2%)	487	0.613 (1.00)	0.711 (1.00)	0.0447 (0.337)	0.866 (1.00)	0.0201 (0.222)	1 (1.00)	0.742 (1.00)	1 (1.00)	0.00303 (0.116)	1 (1.00)	0.078 (0.438)	0.451 (1.00)	0.0112 (0.181)	0.779 (1.00)	0.931 (1.00)	1 (1.00)	1 (1.00)
del 2q22 1	10 (2%)	489	0.614 (1.00)	0.264 (0.806)	0.0255 (0.254)	0.795 (1.00)	0.0149 (0.201)	1 (1.00)	0.732 (1.00)	0.493 (1.00)	0.00519 (0.151)	1 (1.00)	0.15 (0.625)	0.451 (1.00)	0.00672 (0.156)	1 (1.00)	0.349 (0.904)	1 (1.00)	1 (1.00)
del 9q22 33	27 (5%)	472	0.0504 (0.345)	0.000623 (0.06)	0.00055 (0.06)	0.117 (0.541)	0.294 (0.848)	0.3 (0.849)	0.503 (1.00)	0.666 (1.00)	1 (1.00)	1 (1.00)	0.0919 (0.473)	0.823 (1.00)	0.89 (1.00)	0.692 (1.00)	0.0189 (0.219)	0.83 (1.00)	1 (1.00)
amp 4q28 2	6 (1%)	493	0.00905 (0.175)	0.0591 (0.378)	0.332 (0.874)	0.535 (1.00)	0.0302 (0.272)	1 (1.00)	0.662 (1.00)	0.645 (1.00)	0.244 (0.773)	1 (1.00)	1 (1.00)	0.458 (1.00)	0.0224 (0.233)	0.0991 (0.492)	0.236 (0.763)	0.583 (1.00)	1 (1.00)
amp 4q32 3	7 (1%)	492	0.0994 (0.492)	0.118 (0.542)	0.191 (0.696)	0.299 (0.849)	0.0149 (0.201)	1 (1.00)	1 (1.00)	1 (1.00)	0.163 (0.646)	1 (1.00)	1 (1.00)	0.0479 (0.343)	0.00672 (0.156)	0.708 (1.00)	0.266 (0.807)	1 (1.00)	1 (1.00)
amp 6p22 2	4 (1%)	495	2.68e-07 (0.000437)	0.00456 (0.141)	0.0389 (0.305)	0.401 (0.963)	0.623 (1.00)	1 (1.00)	1 (1.00)	0.645 (1.00)	1 (1.00)	1 (1.00)	0.642 (1.00)	1 (1.00)	0.47 (1.00)	0.628 (1.00)	0.294 (0.848)	1 (1.00)	1 (1.00)
amp 6p21 31	3 (1%)	496	0.00635 (0.156)	0.0483 (0.343)	0.0121 (0.184)	0.155 (0.636)	1 (1.00)	0.0618 (0.379)	1 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)		0.454 (1.00)	0.472 (1.00)	1 (1.00)	0.524 (1.00)	0.483 (1.00)	1 (1.00)
amp 7q31 1	22 (4%)	477	0.53 (1.00)	0.0732 (0.427)	0.0294 (0.268)	0.706 (1.00)	0.0716 (0.421)	1 (1.00)	1 (1.00)	0.477 (1.00)	0.0105 (0.175)	1 (1.00)	0.0278 (0.262)	0.154 (0.634)	0.0104 (0.175)	1 (1.00)	0.649 (1.00)	1 (1.00)	0.608 (1.00)
amp 18q22 3	8 (2%)	491	0.58 (1.00)	0.963 (1.00)	1 (1.00)	0.51 (1.00)	0.0149 (0.201)	1 (1.00)	1 (1.00)	0.439 (1.00)	0.511 (1.00)	1 (1.00)	0.759 (1.00)	0.527 (1.00)	0.0122 (0.184)	0.298 (0.849)	0.452 (1.00)	0.758 (1.00)	1 (1.00)
amp xq22 3	15 (3%)	484	0.155 (0.634)	0.375 (0.953)	0.18 (0.672)	0.575 (1.00)	0.416 (0.991)	1 (1.00)	0.0147 (0.201)	0.579 (1.00)	0.513 (1.00)	1 (1.00)	0.0101 (0.175)	0.791 (1.00)	0.311 (0.86)	0.302 (0.849)	0.77 (1.00)	0.797 (1.00)	1 (1.00)
amp xq28	10 (2%)	489	0.176 (0.669)	0.0205 (0.224)	0.0565 (0.371)	0.161 (0.646)	0.503 (1.00)	1 (1.00)	0.0691 (0.411)	0.717 (1.00)	0.123 (0.546)	1 (1.00)	0.00984 (0.175)	0.344 (0.896)	0.214 (0.739)	0.524 (1.00)	0.379 (0.957)	1 (1.00)	1 (1.00)
del 2q37 3	13 (3%)	486	0.25 (0.782)	0.139 (0.596)	0.0123 (0.184)	0.444 (1.00)	0.0372 (0.296)	1 (1.00)	0.349 (0.904)	0.383 (0.958)	0.0495 (0.343)	0.383 (0.958)	0.237 (0.763)	0.233 (0.763)	0.0158 (0.207)	0.779 (1.00)	0.0524 (0.352)	0.758 (1.00)	1 (1.00)
del 6q22 31	7 (1%)	492	0.00235 (0.112)	0.0819 (0.453)	0.189 (0.692)	0.793 (1.00)	0.372 (0.946)		0.392 (0.962)	0.162 (0.646)	0.817 (1.00)	0.213 (0.739)	0.397 (0.962)	0.756 (1.00)	0.176 (0.669)	0.46 (1.00)	0.00914 (0.175)	1 (1.00)	1 (1.00)
del 9p21 3	20 (4%)	479	0.0339 (0.283)	0.00966 (0.175)	0.00024 (0.0356)	0.178 (0.671)	1 (1.00)	0.202 (0.717)	0.441 (1.00)	0.609 (1.00)	0.638 (1.00)	1 (1.00)	0.0598 (0.378)	0.478 (1.00)	0.125 (0.551)	0.172 (0.666)	0.105 (0.512)	0.888 (1.00)	0.379 (0.957)
del 10q23 31	12 (2%)	487	0.567 (1.00)	0.206 (0.728)	0.0442 (0.334)	0.766 (1.00)	0.0201 (0.222)	1 (1.00)	0.319 (0.87)	0.541 (1.00)	0.343 (0.893)	1 (1.00)	0.707 (1.00)	0.623 (1.00)	0.0275 (0.262)	1 (1.00)	0.00234 (0.112)	1 (1.00)	1 (1.00)
del 13q12 13	18 (4%)	481	0.0306 (0.272)	0.00677 (0.156)	0.282 (0.837)	1 (1.00)	0.112 (0.535)	1 (1.00)	0.278 (0.832)	0.424 (1.00)	0.589 (1.00)	0.00275 (0.113)	0.464 (1.00)	1 (1.00)	0.213 (0.739)	0.812 (1.00)	0.58 (1.00)	1 (1.00)	0.623 (1.00)
del 13q22 1	19 (4%)	480	0.0357 (0.293)	0.0841 (0.458)	0.613 (1.00)	0.949 (1.00)	0.0191 (0.219)	1 (1.00)	0.303 (0.849)	1 (1.00)	0.648 (1.00)	0.00275 (0.113)	0.478 (1.00)	0.743 (1.00)	0.0252 (0.254)	0.641 (1.00)	0.377 (0.955)	0.594 (1.00)	0.383 (0.958)
del 16q23 3	6 (1%)	493	0.197 (0.708)	0.0506 (0.345)	0.00219 (0.112)	0.0159 (0.208)	0.449 (1.00)	0.12 (0.546)	1 (1.00)	0.412 (0.981)	0.16 (0.645)	0.213 (0.739)	0.0628 (0.384)	0.0709 (0.418)	0.859 (1.00)	1 (1.00)	0.42 (0.998)	0.472 (1.00)	1 (1.00)
amp 1p36 32	5 (1%)	494	0.673 (1.00)	0.331 (0.874)	0.171 (0.666)	0.232 (0.763)	0.685 (1.00)	1 (1.00)	1 (1.00)	0.645 (1.00)	0.0912 (0.473)	0.181 (0.672)	0.301 (0.849)	0.636 (1.00)	0.897 (1.00)	1 (1.00)	0.0808 (0.451)	0.00696 (0.158)	1 (1.00)
amp 1p32 3	5 (1%)	494	0.724 (1.00)	0.86 (1.00)	0.248 (0.777)	0.892 (1.00)	0.685 (1.00)		0.614 (1.00)	1 (1.00)	0.0722 (0.422)	0.00818 (0.167)	0.696 (1.00)	0.387 (0.962)	0.785 (1.00)	0.665 (1.00)	0.248 (0.777)	1 (1.00)	1 (1.00)
amp 3p14 1	5 (1%)	494	0.014 (0.201)	0.463 (1.00)	0.07 (0.416)	0.285 (0.838)	1 (1.00)	0.0915 (0.473)	1 (1.00)	1 (1.00)	0.561 (1.00)	0.181 (0.672)	1 (1.00)	0.101 (0.497)	0.58 (1.00)	1 (1.00)	0.673 (1.00)	0.483 (1.00)	1 (1.00)
amp 4q31 21	10 (2%)	489	0.228 (0.76)	0.0579 (0.373)	0.157 (0.64)	0.503 (1.00)	0.0372 (0.296)	1 (1.00)	1 (1.00)	1 (1.00)	0.514 (1.00)	1 (1.00)	0.654 (1.00)	0.687 (1.00)	0.0061 (0.156)	0.198 (0.708)	0.182 (0.674)	0.0374 (0.296)	1 (1.00)
amp 6p22 3	3 (1%)	496	0.000698 (0.06)	0.279 (0.832)	0.329 (0.874)	1 (1.00)	0.248 (0.777)	1 (1.00)	1 (1.00)	0.563 (1.00)	1 (1.00)	1 (1.00)	0.61 (1.00)	1 (1.00)		0.253 (0.784)		0.48 (1.00)	1 (1.00)
amp 9q31 1	6 (1%)	493	0.109 (0.526)	0.0471 (0.342)	0.0989 (0.492)	0.314 (0.861)	0.685 (1.00)	1 (1.00)	0.662 (1.00)	1 (1.00)	0.243 (0.772)	1 (1.00)	0.748 (1.00)	1 (1.00)	0.514 (1.00)	1 (1.00)	0.0107 (0.176)	1 (1.00)	1 (1.00)
amp 9q34 3	7 (1%)	492	0.601 (1.00)	0.237 (0.763)	0.234 (0.763)	0.422 (0.999)	0.449 (1.00)	1 (1.00)	0.392 (0.962)	0.682 (1.00)	0.0262 (0.256)	1 (1.00)	0.262 (0.805)	1 (1.00)	0.198 (0.708)	0.708 (1.00)	0.00874 (0.174)	1 (1.00)	1 (1.00)
amp 13q34	7 (1%)	492	0.644 (1.00)	0.235 (0.763)	0.158 (0.644)	0.928 (1.00)	0.216 (0.739)	1 (1.00)	1 (1.00)	1 (1.00)	0.0112 (0.181)	1 (1.00)	0.748 (1.00)	1 (1.00)	0.0776 (0.438)	0.708 (1.00)	0.645 (1.00)	1 (1.00)	1 (1.00)
amp 14q12	13 (3%)	486	0.508 (1.00)	0.0368 (0.296)	0.0212 (0.229)	0.632 (1.00)	0.105 (0.512)	1 (1.00)	0.529 (1.00)	0.057 (0.371)	0.152 (0.631)	1 (1.00)	0.863 (1.00)	0.557 (1.00)	0.15 (0.625)	0.274 (0.825)	0.296 (0.849)	0.399 (0.962)	1 (1.00)
amp 19p13 3	8 (2%)	491	0.698 (1.00)	0.127 (0.556)	0.326 (0.874)	0.378 (0.955)	0.122 (0.546)	1 (1.00)	0.448 (1.00)	0.256 (0.79)	0.0104 (0.175)	1 (1.00)	1 (1.00)	0.586 (1.00)	0.0616 (0.379)	0.48 (1.00)	0.0899 (0.473)	0.236 (0.763)	1 (1.00)
amp 22q11 21	7 (1%)	492	0.795 (1.00)	0.817 (1.00)	0.225 (0.757)	0.613 (1.00)	1 (1.00)	1 (1.00)	0.198 (0.708)	1 (1.00)	0.382 (0.958)	1 (1.00)	0.747 (1.00)	0.0129 (0.191)	0.696 (1.00)	1 (1.00)	0.213 (0.739)	0.318 (0.869)	0.397 (0.962)
amp xq21 2	9 (2%)	490	0.0912 (0.473)	0.0648 (0.394)	0.0349 (0.289)	0.163 (0.646)	0.724 (1.00)	1 (1.00)	0.456 (1.00)	0.711 (1.00)	0.324 (0.874)	1 (1.00)	0.00918 (0.175)	0.0999 (0.492)	0.399 (0.962)	0.739 (1.00)	0.173 (0.666)	1 (1.00)	1 (1.00)
amp xq23	9 (2%)	490	0.0675 (0.409)	0.258 (0.795)	0.0496 (0.343)	0.611 (1.00)	0.724 (1.00)	1 (1.00)	0.456 (1.00)	0.711 (1.00)	0.327 (0.874)	1 (1.00)	0.0194 (0.219)	0.239 (0.765)	0.193 (0.703)	0.313 (0.86)	0.154 (0.634)	1 (1.00)	1 (1.00)
del 8q24 22	7 (1%)	492	0.75 (1.00)	0.409 (0.978)	0.115 (0.539)	0.792 (1.00)	0.0611 (0.378)	1 (1.00)	0.017 (0.214)	0.439 (1.00)	0.163 (0.646)	1 (1.00)	0.756 (1.00)	0.528 (1.00)	0.0414 (0.318)	1 (1.00)	0.27 (0.818)	1 (1.00)	1 (1.00)
del 10p12 31	7 (1%)	492	0.621 (1.00)	0.59 (1.00)	0.385 (0.959)	0.739 (1.00)	0.0302 (0.272)	1 (1.00)	0.392 (0.962)	1 (1.00)	0.819 (1.00)	1 (1.00)	0.762 (1.00)	1 (1.00)	0.0224 (0.233)	0.708 (1.00)	0.0818 (0.453)	0.733 (1.00)	1 (1.00)
del 17p13 1	8 (2%)	491	0.569 (1.00)	0.901 (1.00)	0.145 (0.614)	0.0311 (0.276)	0.724 (1.00)	1 (1.00)	1 (1.00)	0.717 (1.00)	0.235 (0.763)	0.274 (0.825)	0.0598 (0.378)	0.34 (0.888)	0.91 (1.00)	0.731 (1.00)	0.0141 (0.201)	0.581 (1.00)	1 (1.00)
del 19p13 2	7 (1%)	492	0.13 (0.564)	0.166 (0.656)	0.494 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.392 (0.962)	0.682 (1.00)	1 (1.00)	0.0267 (0.258)	1 (1.00)	0.189 (0.692)		0.46 (1.00)	0.00278 (0.113)	0.761 (1.00)	1 (1.00)
del 19p13 12	8 (2%)	491	0.0998 (0.492)	0.263 (0.806)	0.266 (0.807)	0.88 (1.00)	0.623 (1.00)	1 (1.00)	0.448 (1.00)	1 (1.00)	1 (1.00)	0.0267 (0.258)	0.603 (1.00)	0.28 (0.834)		1 (1.00)	0.00769 (0.161)	0.138 (0.593)	1 (1.00)
del 21q21 1	9 (2%)	490	0.68 (1.00)	0.107 (0.516)	0.00675 (0.156)	0.265 (0.807)	1 (1.00)	1 (1.00)	0.707 (1.00)	1 (1.00)	0.65 (1.00)	1 (1.00)	0.624 (1.00)	0.397 (0.962)	0.741 (1.00)	0.313 (0.86)	0.465 (1.00)	0.295 (0.849)	1 (1.00)
del xq23	4 (1%)	495	0.749 (1.00)	0.223 (0.754)	0.00094 (0.0767)	0.0487 (0.343)	0.123 (0.546)		0.0611 (0.378)	0.16 (0.645)	1 (1.00)	0.112 (0.535)	0.645 (1.00)	0.313 (0.86)	0.0414 (0.318)	1 (1.00)	0.656 (1.00)		1 (1.00)
del xq22 3	4 (1%)	495	0.749 (1.00)	0.223 (0.754)	0.00101 (0.0785)	0.0477 (0.343)	0.123 (0.546)		0.0611 (0.378)	0.16 (0.645)	1 (1.00)	0.112 (0.535)	0.644 (1.00)	0.311 (0.86)	0.0414 (0.318)	1 (1.00)	0.656 (1.00)		1 (1.00)
amp 1p31 1	5 (1%)	494	0.722 (1.00)	0.617 (1.00)	0.122 (0.546)	0.707 (1.00)	0.216 (0.739)	1 (1.00)	0.123 (0.546)	0.285 (0.838)	0.0473 (0.342)	0.147 (0.619)	1 (1.00)	0.39 (0.962)	0.818 (1.00)	0.665 (1.00)	0.399 (0.962)	1 (1.00)	1 (1.00)
amp 2p16 1	3 (1%)	496	0.687 (1.00)	0.799 (1.00)	0.503 (1.00)	0.583 (1.00)	1 (1.00)	1 (1.00)	0.177 (0.669)	1 (1.00)	0.0776 (0.438)	1 (1.00)	1 (1.00)	0.233 (0.763)		1 (1.00)	0.514 (1.00)	0.482 (1.00)	1 (1.00)
amp 2q37 2	3 (1%)	496	0.821 (1.00)	0.541 (1.00)	1 (1.00)	0.393 (0.962)	1 (1.00)	1 (1.00)	1 (1.00)	0.563 (1.00)	0.14 (0.598)	1 (1.00)				1 (1.00)		1 (1.00)	1 (1.00)
amp 6p21 2	4 (1%)	495	0.0256 (0.254)	0.885 (1.00)	0.638 (1.00)	0.633 (1.00)	0.623 (1.00)	1 (1.00)	1 (1.00)	0.304 (0.851)	0.708 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.125 (0.55)	0.628 (1.00)	0.202 (0.717)	0.583 (1.00)	0.332 (0.874)
amp 6p12 2	3 (1%)	496	0.0256 (0.254)	0.241 (0.769)	0.329 (0.874)	0.698 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.614 (1.00)	1 (1.00)	0.331 (0.874)	0.253 (0.784)	0.524 (1.00)	1 (1.00)	1 (1.00)
amp 6q12	3 (1%)	496	0.829 (1.00)	0.253 (0.784)	0.603 (1.00)	1 (1.00)	0.623 (1.00)	1 (1.00)	0.568 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.762 (1.00)	0.253 (0.784)		1 (1.00)	1 (1.00)
amp 6q27	4 (1%)	495	0.625 (1.00)	0.4 (0.963)	0.0877 (0.466)	0.149 (0.624)	1 (1.00)	1 (1.00)	0.578 (1.00)	0.645 (1.00)	0.455 (1.00)	0.147 (0.619)	0.0948 (0.481)	0.313 (0.86)	0.527 (1.00)	0.128 (0.558)	0.142 (0.602)	1 (1.00)	1 (1.00)
amp 9q22 31	6 (1%)	493	0.673 (1.00)	0.0874 (0.466)	0.099 (0.492)	0.332 (0.874)	0.685 (1.00)	1 (1.00)	0.35 (0.904)	0.653 (1.00)	0.12 (0.546)	0.181 (0.672)	0.496 (1.00)	0.463 (1.00)	0.542 (1.00)	0.0991 (0.492)	0.0518 (0.349)	1 (1.00)	1 (1.00)
amp 10q25 1	4 (1%)	495	0.715 (1.00)	0.281 (0.836)	0.735 (1.00)	0.56 (1.00)	0.623 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.141 (0.599)	1 (1.00)	1 (1.00)	0.0489 (0.343)	0.29 (0.846)	1 (1.00)	0.301 (0.849)		1 (1.00)
amp 11p13	8 (2%)	491	0.544 (1.00)	0.873 (1.00)	0.33 (0.874)	0.828 (1.00)	0.216 (0.739)	1 (1.00)	0.448 (1.00)	0.717 (1.00)	0.509 (1.00)	1 (1.00)	0.601 (1.00)	0.586 (1.00)	0.119 (0.546)	0.298 (0.849)	0.677 (1.00)	0.171 (0.666)	1 (1.00)
amp 13q14 2	6 (1%)	493	0.74 (1.00)	0.476 (1.00)	0.117 (0.541)	0.702 (1.00)	0.372 (0.946)	1 (1.00)	1 (1.00)	0.682 (1.00)	0.242 (0.771)	1 (1.00)	1 (1.00)	1 (1.00)	0.0414 (0.318)	1 (1.00)	0.91 (1.00)	0.48 (1.00)	1 (1.00)
amp 18q12 1	7 (1%)	492	0.616 (1.00)	0.949 (1.00)	0.882 (1.00)	1 (1.00)	0.216 (0.739)	1 (1.00)	1 (1.00)	0.682 (1.00)	1 (1.00)	1 (1.00)	0.75 (1.00)	0.462 (1.00)	0.0949 (0.481)	0.46 (1.00)	0.467 (1.00)	1 (1.00)	1 (1.00)
amp 18q22 1	7 (1%)	492	0.609 (1.00)	0.978 (1.00)	0.882 (1.00)	0.695 (1.00)	0.216 (0.739)	1 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.748 (1.00)	0.316 (0.865)	0.301 (0.849)	1 (1.00)	0.775 (1.00)	1 (1.00)	1 (1.00)
amp 21q21 3	6 (1%)	493	0.617 (1.00)	0.538 (1.00)	0.843 (1.00)	0.639 (1.00)	0.123 (0.546)	1 (1.00)	0.662 (1.00)	0.214 (0.739)	1 (1.00)	1 (1.00)	1 (1.00)	0.242 (0.771)	0.0778 (0.438)	0.0333 (0.281)	0.126 (0.553)	1 (1.00)	1 (1.00)
amp xp11 22	8 (2%)	491	0.0513 (0.347)	0.0495 (0.343)	0.0328 (0.281)	0.398 (0.962)	0.449 (1.00)	1 (1.00)	0.688 (1.00)	1 (1.00)	0.24 (0.767)	0.274 (0.825)	0.026 (0.256)	0.238 (0.763)	0.118 (0.542)	0.48 (1.00)	0.177 (0.669)	0.666 (1.00)	1 (1.00)
amp xp11 21	9 (2%)	490	0.3 (0.849)	0.0323 (0.28)	0.0282 (0.262)	0.352 (0.906)	0.449 (1.00)	1 (1.00)	0.121 (0.546)	1 (1.00)	0.094 (0.481)	1 (1.00)	0.0332 (0.281)	0.0839 (0.458)	0.131 (0.568)	1 (1.00)	0.197 (0.708)	1 (1.00)	0.455 (1.00)
amp xq24	9 (2%)	490	0.159 (0.645)	0.0754 (0.436)	0.0284 (0.262)	0.612 (1.00)	0.285 (0.838)	1 (1.00)	0.121 (0.546)	0.711 (1.00)	0.184 (0.677)	1 (1.00)	0.0336 (0.282)	0.29 (0.846)	0.0921 (0.473)	0.739 (1.00)	0.262 (0.805)	1 (1.00)	1 (1.00)
amp xq24	9 (2%)	490	0.0912 (0.473)	0.184 (0.677)	0.049 (0.343)	0.562 (1.00)	0.724 (1.00)	1 (1.00)	0.121 (0.546)	0.711 (1.00)	0.324 (0.874)	1 (1.00)	0.034 (0.283)	0.292 (0.848)	0.524 (1.00)	0.313 (0.86)	0.81 (1.00)	1 (1.00)	1 (1.00)
del 1q24 2	3 (1%)	496	0.677 (1.00)	0.822 (1.00)	0.328 (0.874)	0.808 (1.00)	0.499 (1.00)		0.568 (1.00)	0.523 (1.00)	0.227 (0.758)	1 (1.00)	0.613 (1.00)	1 (1.00)		1 (1.00)	0.117 (0.541)		1 (1.00)
del 1q42 13	5 (1%)	494	0.571 (1.00)	0.461 (1.00)	0.794 (1.00)	0.511 (1.00)	0.623 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.559 (1.00)	1 (1.00)	1 (1.00)	0.637 (1.00)	0.394 (0.962)	1 (1.00)	0.0423 (0.324)	1 (1.00)	0.0474 (0.342)
del 4q34 3	5 (1%)	494	0.597 (1.00)	0.742 (1.00)	0.115 (0.539)	0.176 (0.669)	0.623 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.563 (1.00)	1 (1.00)	0.136 (0.589)	1 (1.00)	0.29 (0.846)	0.38 (0.958)	0.0533 (0.356)	0.581 (1.00)	1 (1.00)
del 5p15 2	4 (1%)	495	0.858 (1.00)	0.182 (0.674)	0.223 (0.754)	0.634 (1.00)	0.372 (0.946)	1 (1.00)	0.578 (1.00)	0.645 (1.00)	0.23 (0.763)	1 (1.00)	0.422 (0.999)	0.0691 (0.411)	0.859 (1.00)	0.338 (0.885)	0.21 (0.737)	0.318 (0.869)	0.332 (0.874)
del 7q34	4 (1%)	495	0.708 (1.00)	0.757 (1.00)	0.472 (1.00)	0.505 (1.00)	0.623 (1.00)	1 (1.00)	1 (1.00)	0.645 (1.00)	0.14 (0.599)	1 (1.00)	0.645 (1.00)	1 (1.00)	0.472 (1.00)	0.628 (1.00)	0.0875 (0.466)	1 (1.00)	1 (1.00)
del 8p23 2	4 (1%)	495	0.816 (1.00)	0.913 (1.00)	0.17 (0.666)	0.87 (1.00)	0.248 (0.777)	1 (1.00)	0.0611 (0.378)	0.645 (1.00)	0.456 (1.00)	1 (1.00)	0.643 (1.00)	1 (1.00)	0.0778 (0.438)	1 (1.00)	0.737 (1.00)		1 (1.00)
del 8p22	4 (1%)	495	0.816 (1.00)	0.913 (1.00)	0.171 (0.666)	0.871 (1.00)	0.248 (0.777)	1 (1.00)	0.0611 (0.378)	0.645 (1.00)	0.455 (1.00)	1 (1.00)	0.645 (1.00)	1 (1.00)	0.0778 (0.438)	1 (1.00)	0.737 (1.00)		1 (1.00)
del 8p12	4 (1%)	495	0.816 (1.00)	0.913 (1.00)	0.171 (0.666)	0.869 (1.00)	0.248 (0.777)	1 (1.00)	0.0611 (0.378)	0.645 (1.00)	0.458 (1.00)	1 (1.00)	0.644 (1.00)	1 (1.00)	0.0778 (0.438)	1 (1.00)	0.737 (1.00)		1 (1.00)
del 10q21 2	12 (2%)	487	0.57 (1.00)	0.971 (1.00)	0.828 (1.00)	0.741 (1.00)	0.338 (0.885)	1 (1.00)	0.742 (1.00)	0.541 (1.00)	0.542 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.354 (0.908)	0.761 (1.00)	0.0352 (0.291)	0.843 (1.00)	0.61 (1.00)
del 15q25 3	9 (2%)	490	0.565 (1.00)	0.882 (1.00)	0.277 (0.828)	0.537 (1.00)	0.0679 (0.41)	0.0915 (0.473)	0.456 (1.00)	0.492 (1.00)	0.0917 (0.473)	1 (1.00)	1 (1.00)	1 (1.00)	0.0769 (0.438)	1 (1.00)	0.149 (0.624)	0.666 (1.00)	0.397 (0.962)
del 18q12 3	4 (1%)	495	0.671 (1.00)	0.672 (1.00)	0.172 (0.666)	0.305 (0.851)	1 (1.00)	1 (1.00)	1 (1.00)	0.645 (1.00)	0.457 (1.00)	1 (1.00)	0.643 (1.00)	1 (1.00)	0.331 (0.874)	0.628 (1.00)	0.647 (1.00)		0.182 (0.674)
del 22q12 3	90 (18%)	409	0.236 (0.763)	0.463 (1.00)	0.58 (1.00)	0.887 (1.00)	0.393 (0.962)	0.644 (1.00)	0.358 (0.914)	0.0684 (0.41)	0.18 (0.672)	0.218 (0.743)	0.482 (1.00)	0.305 (0.851)	0.569 (1.00)	0.197 (0.708)	0.652 (1.00)	0.443 (1.00)	1 (1.00)
del 22q13 1	89 (18%)	410	0.237 (0.763)	0.458 (1.00)	0.681 (1.00)	0.863 (1.00)	0.326 (0.874)	0.644 (1.00)	0.43 (1.00)	0.0867 (0.466)	0.168 (0.662)	0.332 (0.874)	0.551 (1.00)	0.294 (0.848)	0.458 (1.00)	0.286 (0.838)	0.579 (1.00)	0.443 (1.00)	1 (1.00)
del 22q13 2	89 (18%)	410	0.237 (0.763)	0.458 (1.00)	0.683 (1.00)	0.862 (1.00)	0.326 (0.874)	0.644 (1.00)	0.43 (1.00)	0.0867 (0.466)	0.17 (0.666)	0.332 (0.874)	0.555 (1.00)	0.293 (0.848)	0.458 (1.00)	0.286 (0.838)	0.579 (1.00)	0.443 (1.00)	1 (1.00)
del 22q13 32	90 (18%)	409	0.236 (0.763)	0.487 (1.00)	0.699 (1.00)	0.887 (1.00)	0.272 (0.821)	0.649 (1.00)	0.511 (1.00)	0.0684 (0.41)	0.114 (0.539)	0.218 (0.743)	0.481 (1.00)	0.293 (0.848)	0.383 (0.958)	0.197 (0.708)	0.579 (1.00)	0.458 (1.00)	1 (1.00)

'amp_1p36.32' versus 'RACE'

P value = 0.00696 (Fisher's exact test), Q value = 0.16

Table S1. Gene #1: 'amp_1p36.32' versus Clinical Feature #16: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	1	52	27	328
AMP PEAK 1(1P36.32) MUTATED	0	0	3	2
AMP PEAK 1(1P36.32) WILD-TYPE	1	52	24	326

Figure S1. Get High-res Image Gene #1: 'amp_1p36.32' versus Clinical Feature #16: 'RACE'

'amp_1p32.3' versus 'RADIATION_EXPOSURE'

P value = 0.00818 (Fisher's exact test), Q value = 0.17

Table S2. Gene #2: 'amp_1p32.3' versus Clinical Feature #10: 'RADIATION_EXPOSURE'

nPatients	NO	YES
ALL	420	17
AMP PEAK 2(1P32.3) MUTATED	2	2
AMP PEAK 2(1P32.3) WILD-TYPE	418	15

Figure S2. Get High-res Image Gene #2: 'amp_1p32.3' versus Clinical Feature #10: 'RADIATION_EXPOSURE'

'amp_1q31.2' versus 'YEARS_TO_BIRTH'

P value = 5.12e-05 (Wilcoxon-test), Q value = 0.0087

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

	nPatients	Mean (Std.Dev)
ALL	499	47.3 (15.8)
AMP PEAK 4(1Q31.2) MUTATED	29	59.9 (17.3)
AMP PEAK 4(1Q31.2) WILD-TYPE	470	46.5 (15.3)

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

'amp_1q31.2' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0027

Table S4. Gene #4: 'amp_1q31.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV	STAGE IVA	STAGE IVC
ALL	282	50	111	2	46	6
AMP PEAK 4(1Q31.2) MUTATED	7	0	12	1	9	0
AMP PEAK 4(1Q31.2) WILD-TYPE	275	50	99	1	37	6

Figure S4. Get High-res Image Gene #4: 'amp_1q31.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'amp_1q31.2' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0027

Table S5. Gene #4: 'amp_1q31.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

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

Figure S5. Get High-res Image Gene #4: 'amp_1q31.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_1q31.2' versus 'PATHOLOGY_N_STAGE'

P value = 0.000629 (Fisher's exact test), Q value = 0.06

Table S6. Gene #4: 'amp_1q31.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	225	224
AMP PEAK 4(1Q31.2) MUTATED	5	22
AMP PEAK 4(1Q31.2) WILD-TYPE	220	202

Figure S6. Get High-res Image Gene #4: 'amp_1q31.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_1q31.2' versus 'HISTOLOGICAL_TYPE'

P value = 0.00636 (Fisher's exact test), Q value = 0.16

Table S7. Gene #4: 'amp_1q31.2' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients	OTHER SPECIFY	THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL	THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)	THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
ALL	8	355	100	36
AMP PEAK 4(1Q31.2) MUTATED	0	25	0	4
AMP PEAK 4(1Q31.2) WILD-TYPE	8	330	100	32

Figure S7. Get High-res Image Gene #4: 'amp_1q31.2' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_1q31.2' versus 'EXTRATHYROIDAL_EXTENSION'

P value = 3e-05 (Fisher's exact test), Q value = 0.007

Table S8. Gene #4: 'amp_1q31.2' versus Clinical Feature #11: 'EXTRATHYROIDAL_EXTENSION'

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

Figure S8. Get High-res Image Gene #4: 'amp_1q31.2' versus Clinical Feature #11: 'EXTRATHYROIDAL_EXTENSION'

'amp_1q31.2' versus 'TUMOR_SIZE'

P value = 0.00305 (Wilcoxon-test), Q value = 0.12

Table S9. Gene #4: 'amp_1q31.2' versus Clinical Feature #15: 'TUMOR_SIZE'

	nPatients	Mean (Std.Dev)
ALL	401	3.0 (1.6)
AMP PEAK 4(1Q31.2) MUTATED	24	3.8 (1.5)
AMP PEAK 4(1Q31.2) WILD-TYPE	377	2.9 (1.6)

Figure S9. Get High-res Image Gene #4: 'amp_1q31.2' versus Clinical Feature #15: 'TUMOR_SIZE'

'amp_1q31.2' versus 'RACE'

P value = 0.0034 (Fisher's exact test), Q value = 0.12

Table S10. Gene #4: 'amp_1q31.2' versus Clinical Feature #16: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	1	52	27	328
AMP PEAK 4(1Q31.2) MUTATED	1	1	5	21
AMP PEAK 4(1Q31.2) WILD-TYPE	0	51	22	307

Figure S10. Get High-res Image Gene #4: 'amp_1q31.2' versus Clinical Feature #16: 'RACE'

'amp_1q43' versus 'YEARS_TO_BIRTH'

P value = 2.73e-06 (Wilcoxon-test), Q value = 0.0022

Table S11. Gene #5: 'amp_1q43' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	499	47.3 (15.8)
AMP PEAK 5(1Q43) MUTATED	29	61.7 (15.5)
AMP PEAK 5(1Q43) WILD-TYPE	470	46.4 (15.4)

Figure S11. Get High-res Image Gene #5: 'amp_1q43' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_1q43' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0027

Table S12. Gene #5: 'amp_1q43' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV	STAGE IVA	STAGE IVC
ALL	282	50	111	2	46	6
AMP PEAK 5(1Q43) MUTATED	6	0	12	1	9	1
AMP PEAK 5(1Q43) WILD-TYPE	276	50	99	1	37	5

Figure S12. Get High-res Image Gene #5: 'amp_1q43' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'amp_1q43' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0027

Table S13. Gene #5: 'amp_1q43' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	142	165	167	23
AMP PEAK 5(1Q43) MUTATED	2	3	18	6
AMP PEAK 5(1Q43) WILD-TYPE	140	162	149	17

Figure S13. Get High-res Image Gene #5: 'amp_1q43' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_1q43' versus 'PATHOLOGY_N_STAGE'

P value = 0.00166 (Fisher's exact test), Q value = 0.11

Table S14. Gene #5: 'amp_1q43' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	225	224
AMP PEAK 5(1Q43) MUTATED	6	22
AMP PEAK 5(1Q43) WILD-TYPE	219	202

Figure S14. Get High-res Image Gene #5: 'amp_1q43' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_1q43' versus 'HISTOLOGICAL_TYPE'

P value = 0.00594 (Fisher's exact test), Q value = 0.16

Table S15. Gene #5: 'amp_1q43' 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	8	355	100	36
AMP PEAK 5(1Q43) MUTATED	0	25	0	4
AMP PEAK 5(1Q43) WILD-TYPE	8	330	100	32

Figure S15. Get High-res Image Gene #5: 'amp_1q43' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_1q43' versus 'EXTRATHYROIDAL_EXTENSION'

P value = 5e-05 (Fisher's exact test), Q value = 0.0087

Table S16. Gene #5: 'amp_1q43' versus Clinical Feature #11: 'EXTRATHYROIDAL_EXTENSION'

nPatients	MINIMAL (T3)	MODERATE/ADVANCED (T4A)	NONE	VERY ADVANCED (T4B)
ALL	132	18	330	1
AMP PEAK 5(1Q43) MUTATED	14	4	10	1
AMP PEAK 5(1Q43) WILD-TYPE	118	14	320	0

Figure S16. Get High-res Image Gene #5: 'amp_1q43' versus Clinical Feature #11: 'EXTRATHYROIDAL_EXTENSION'

'amp_1q43' versus 'TUMOR_SIZE'

P value = 0.00531 (Wilcoxon-test), Q value = 0.15

Table S17. Gene #5: 'amp_1q43' versus Clinical Feature #15: 'TUMOR_SIZE'

	nPatients	Mean (Std.Dev)
ALL	401	3.0 (1.6)
AMP PEAK 5(1Q43) MUTATED	24	3.8 (1.5)
AMP PEAK 5(1Q43) WILD-TYPE	377	2.9 (1.6)

Figure S17. Get High-res Image Gene #5: 'amp_1q43' versus Clinical Feature #15: 'TUMOR_SIZE'

'amp_1q43' versus 'RACE'

P value = 0.00349 (Fisher's exact test), Q value = 0.12

Table S18. Gene #5: 'amp_1q43' versus Clinical Feature #16: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	1	52	27	328
AMP PEAK 5(1Q43) MUTATED	1	1	5	21
AMP PEAK 5(1Q43) WILD-TYPE	0	51	22	307

Figure S18. Get High-res Image Gene #5: 'amp_1q43' versus Clinical Feature #16: 'RACE'

'amp_3p22.3' versus 'Time to Death'

P value = 0.00231 (logrank test), Q value = 0.11

Table S19. Gene #8: 'amp_3p22.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	497	16	0.2 - 169.3 (30.6)
AMP PEAK 9(3P22.3) MUTATED	4	1	6.0 - 57.6 (12.2)
AMP PEAK 9(3P22.3) WILD-TYPE	493	15	0.2 - 169.3 (30.6)

Figure S19. Get High-res Image Gene #8: 'amp_3p22.3' versus Clinical Feature #1: 'Time to Death'

'amp_3p22.3' versus 'YEARS_TO_BIRTH'

P value = 0.0151 (Wilcoxon-test), Q value = 0.2

Table S20. Gene #8: 'amp_3p22.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	499	47.3 (15.8)
AMP PEAK 9(3P22.3) MUTATED	4	66.5 (9.0)
AMP PEAK 9(3P22.3) WILD-TYPE	495	47.1 (15.7)

Figure S20. Get High-res Image Gene #8: 'amp_3p22.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_3p22.3' versus 'PATHOLOGIC_STAGE'

P value = 0.0096 (Fisher's exact test), Q value = 0.18

Table S21. Gene #8: 'amp_3p22.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV	STAGE IVA	STAGE IVC
ALL	282	50	111	2	46	6
AMP PEAK 9(3P22.3) MUTATED	1	2	0	0	0	1
AMP PEAK 9(3P22.3) WILD-TYPE	281	48	111	2	46	5

Figure S21. Get High-res Image Gene #8: 'amp_3p22.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'amp_3p14.1' versus 'Time to Death'

P value = 0.014 (logrank test), Q value = 0.2

Table S22. Gene #9: 'amp_3p14.1' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	497	16	0.2 - 169.3 (30.6)
AMP PEAK 10(3P14.1) MUTATED	5	1	6.0 - 57.6 (27.4)
AMP PEAK 10(3P14.1) WILD-TYPE	492	15	0.2 - 169.3 (30.6)

Figure S22. Get High-res Image Gene #9: 'amp_3p14.1' versus Clinical Feature #1: 'Time to Death'

'amp_4p16.1' versus 'Time to Death'

P value = 0.0117 (logrank test), Q value = 0.18

Table S23. Gene #10: 'amp_4p16.1' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	497	16	0.2 - 169.3 (30.6)
AMP PEAK 11(4P16.1) MUTATED	7	1	1.0 - 57.0 (13.8)
AMP PEAK 11(4P16.1) WILD-TYPE	490	15	0.2 - 169.3 (30.7)

Figure S23. Get High-res Image Gene #10: 'amp_4p16.1' versus Clinical Feature #1: 'Time to Death'

'amp_4p16.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.0149 (Fisher's exact test), Q value = 0.2

Table S24. Gene #10: 'amp_4p16.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	225	224
AMP PEAK 11(4P16.1) MUTATED	7	0
AMP PEAK 11(4P16.1) WILD-TYPE	218	224

Figure S24. Get High-res Image Gene #10: 'amp_4p16.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_4p16.1' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0122 (Wilcoxon-test), Q value = 0.18

Table S25. Gene #10: 'amp_4p16.1' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	385	3.6 (6.0)
AMP PEAK 11(4P16.1) MUTATED	6	0.0 (0.0)
AMP PEAK 11(4P16.1) WILD-TYPE	379	3.6 (6.0)

Figure S25. Get High-res Image Gene #10: 'amp_4p16.1' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'amp_4q28.2' versus 'Time to Death'

P value = 0.00905 (logrank test), Q value = 0.17

Table S26. Gene #11: 'amp_4q28.2' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	497	16	0.2 - 169.3 (30.6)
AMP PEAK 12(4Q28.2) MUTATED	6	1	1.0 - 57.0 (14.1)
AMP PEAK 12(4Q28.2) WILD-TYPE	491	15	0.2 - 169.3 (30.6)

Figure S26. Get High-res Image Gene #11: 'amp_4q28.2' versus Clinical Feature #1: 'Time to Death'

'amp_4q28.2' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0224 (Wilcoxon-test), Q value = 0.23

Table S27. Gene #11: 'amp_4q28.2' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	385	3.6 (6.0)
AMP PEAK 12(4Q28.2) MUTATED	5	0.0 (0.0)
AMP PEAK 12(4Q28.2) WILD-TYPE	380	3.6 (6.0)

Figure S27. Get High-res Image Gene #11: 'amp_4q28.2' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'amp_4q31.21' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0061 (Wilcoxon-test), Q value = 0.16

Table S28. Gene #12: 'amp_4q31.21' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	385	3.6 (6.0)
AMP PEAK 13(4Q31.21) MUTATED	9	0.1 (0.3)
AMP PEAK 13(4Q31.21) WILD-TYPE	376	3.6 (6.0)

Figure S28. Get High-res Image Gene #12: 'amp_4q31.21' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'amp_4q32.3' versus 'PATHOLOGY_N_STAGE'

P value = 0.0149 (Fisher's exact test), Q value = 0.2

Table S29. Gene #13: 'amp_4q32.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	225	224
AMP PEAK 14(4Q32.3) MUTATED	7	0
AMP PEAK 14(4Q32.3) WILD-TYPE	218	224

Figure S29. Get High-res Image Gene #13: 'amp_4q32.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_4q32.3' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00672 (Wilcoxon-test), Q value = 0.16

Table S30. Gene #13: 'amp_4q32.3' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	385	3.6 (6.0)
AMP PEAK 14(4Q32.3) MUTATED	7	0.0 (0.0)
AMP PEAK 14(4Q32.3) WILD-TYPE	378	3.6 (6.0)

Figure S30. Get High-res Image Gene #13: 'amp_4q32.3' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'amp_5p14.3' versus 'YEARS_TO_BIRTH'

P value = 5.33e-05 (Wilcoxon-test), Q value = 0.0087

Table S31. Gene #14: 'amp_5p14.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	499	47.3 (15.8)
AMP PEAK 15(5P14.3) MUTATED	23	61.1 (15.0)
AMP PEAK 15(5P14.3) WILD-TYPE	476	46.6 (15.5)

Figure S31. Get High-res Image Gene #14: 'amp_5p14.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_5p14.3' versus 'PATHOLOGIC_STAGE'

P value = 0.00141 (Fisher's exact test), Q value = 0.1

Table S32. Gene #14: 'amp_5p14.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV	STAGE IVA	STAGE IVC
ALL	282	50	111	2	46	6
AMP PEAK 15(5P14.3) MUTATED	5	5	8	1	4	0
AMP PEAK 15(5P14.3) WILD-TYPE	277	45	103	1	42	6

Figure S32. Get High-res Image Gene #14: 'amp_5p14.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'amp_5p14.3' versus 'TUMOR_SIZE'

P value = 0.0162 (Wilcoxon-test), Q value = 0.21

Table S33. Gene #14: 'amp_5p14.3' versus Clinical Feature #15: 'TUMOR_SIZE'

	nPatients	Mean (Std.Dev)
ALL	401	3.0 (1.6)
AMP PEAK 15(5P14.3) MUTATED	22	3.7 (1.6)
AMP PEAK 15(5P14.3) WILD-TYPE	379	2.9 (1.6)

Figure S33. Get High-res Image Gene #14: 'amp_5p14.3' versus Clinical Feature #15: 'TUMOR_SIZE'

'amp_5q21.1' versus 'YEARS_TO_BIRTH'

P value = 0.022 (Wilcoxon-test), Q value = 0.23

Table S34. Gene #15: 'amp_5q21.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	499	47.3 (15.8)
AMP PEAK 16(5Q21.1) MUTATED	23	54.7 (15.1)
AMP PEAK 16(5Q21.1) WILD-TYPE	476	46.9 (15.7)

Figure S34. Get High-res Image Gene #15: 'amp_5q21.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_5q21.1' versus 'PATHOLOGIC_STAGE'

P value = 0.00763 (Fisher's exact test), Q value = 0.16

Table S35. Gene #15: 'amp_5q21.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV	STAGE IVA	STAGE IVC
ALL	282	50	111	2	46	6
AMP PEAK 16(5Q21.1) MUTATED	8	7	5	1	2	0
AMP PEAK 16(5Q21.1) WILD-TYPE	274	43	106	1	44	6

Figure S35. Get High-res Image Gene #15: 'amp_5q21.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'amp_5q21.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.0168 (Fisher's exact test), Q value = 0.21

Table S36. Gene #15: 'amp_5q21.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	225	224
AMP PEAK 16(5Q21.1) MUTATED	15	4
AMP PEAK 16(5Q21.1) WILD-TYPE	210	220

Figure S36. Get High-res Image Gene #15: 'amp_5q21.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_5q21.1' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00813 (Wilcoxon-test), Q value = 0.17

Table S37. Gene #15: 'amp_5q21.1' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	385	3.6 (6.0)
AMP PEAK 16(5Q21.1) MUTATED	15	0.8 (1.9)
AMP PEAK 16(5Q21.1) WILD-TYPE	370	3.7 (6.1)

Figure S37. Get High-res Image Gene #15: 'amp_5q21.1' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'amp_5q21.1' versus 'YEARS_TO_BIRTH'

P value = 0.00197 (Wilcoxon-test), Q value = 0.11

Table S38. Gene #16: 'amp_5q21.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	499	47.3 (15.8)
AMP PEAK 17(5Q21.1) MUTATED	20	57.9 (13.7)
AMP PEAK 17(5Q21.1) WILD-TYPE	479	46.8 (15.7)

Figure S38. Get High-res Image Gene #16: 'amp_5q21.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_5q21.1' versus 'PATHOLOGIC_STAGE'

P value = 0.00068 (Fisher's exact test), Q value = 0.06

Table S39. Gene #16: 'amp_5q21.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV	STAGE IVA	STAGE IVC
ALL	282	50	111	2	46	6
AMP PEAK 17(5Q21.1) MUTATED	5	7	6	1	1	0
AMP PEAK 17(5Q21.1) WILD-TYPE	277	43	105	1	45	6

Figure S39. Get High-res Image Gene #16: 'amp_5q21.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'amp_5q21.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.00358 (Fisher's exact test), Q value = 0.12

Table S40. Gene #16: 'amp_5q21.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	225	224
AMP PEAK 17(5Q21.1) MUTATED	14	2
AMP PEAK 17(5Q21.1) WILD-TYPE	211	222

Figure S40. Get High-res Image Gene #16: 'amp_5q21.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_5q21.1' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00192 (Wilcoxon-test), Q value = 0.11

Table S41. Gene #16: 'amp_5q21.1' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	385	3.6 (6.0)
AMP PEAK 17(5Q21.1) MUTATED	13	0.5 (1.9)
AMP PEAK 17(5Q21.1) WILD-TYPE	372	3.7 (6.1)

Figure S41. Get High-res Image Gene #16: 'amp_5q21.1' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'amp_5q21.1' versus 'TUMOR_SIZE'

P value = 0.0116 (Wilcoxon-test), Q value = 0.18

Table S42. Gene #16: 'amp_5q21.1' versus Clinical Feature #15: 'TUMOR_SIZE'

	nPatients	Mean (Std.Dev)
ALL	401	3.0 (1.6)
AMP PEAK 17(5Q21.1) MUTATED	19	3.9 (1.8)
AMP PEAK 17(5Q21.1) WILD-TYPE	382	2.9 (1.6)

Figure S42. Get High-res Image Gene #16: 'amp_5q21.1' versus Clinical Feature #15: 'TUMOR_SIZE'

'amp_5q33.1' versus 'YEARS_TO_BIRTH'

P value = 0.0131 (Wilcoxon-test), Q value = 0.19

Table S43. Gene #17: 'amp_5q33.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	499	47.3 (15.8)
AMP PEAK 18(5Q33.1) MUTATED	21	55.7 (14.8)
AMP PEAK 18(5Q33.1) WILD-TYPE	478	46.9 (15.7)

Figure S43. Get High-res Image Gene #17: 'amp_5q33.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_5q33.1' versus 'PATHOLOGIC_STAGE'

P value = 0.00379 (Fisher's exact test), Q value = 0.12

Table S44. Gene #17: 'amp_5q33.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV	STAGE IVA	STAGE IVC
ALL	282	50	111	2	46	6
AMP PEAK 18(5Q33.1) MUTATED	7	7	5	1	1	0
AMP PEAK 18(5Q33.1) WILD-TYPE	275	43	106	1	45	6

Figure S44. Get High-res Image Gene #17: 'amp_5q33.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'amp_5q33.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.0191 (Fisher's exact test), Q value = 0.22

Table S45. Gene #17: 'amp_5q33.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	225	224
AMP PEAK 18(5Q33.1) MUTATED	13	3
AMP PEAK 18(5Q33.1) WILD-TYPE	212	221

Figure S45. Get High-res Image Gene #17: 'amp_5q33.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_5q33.1' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0101 (Wilcoxon-test), Q value = 0.18

Table S46. Gene #17: 'amp_5q33.1' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	385	3.6 (6.0)
AMP PEAK 18(5Q33.1) MUTATED	14	1.4 (3.8)
AMP PEAK 18(5Q33.1) WILD-TYPE	371	3.6 (6.0)

Figure S46. Get High-res Image Gene #17: 'amp_5q33.1' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'amp_5q35.2' versus 'YEARS_TO_BIRTH'

P value = 0.00287 (Wilcoxon-test), Q value = 0.11

Table S47. Gene #18: 'amp_5q35.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	499	47.3 (15.8)
AMP PEAK 19(5Q35.2) MUTATED	20	57.5 (13.8)
AMP PEAK 19(5Q35.2) WILD-TYPE	479	46.8 (15.7)

Figure S47. Get High-res Image Gene #18: 'amp_5q35.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_5q35.2' versus 'PATHOLOGIC_STAGE'

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

Table S48. Gene #18: 'amp_5q35.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV	STAGE IVA	STAGE IVC
ALL	282	50	111	2	46	6
AMP PEAK 19(5Q35.2) MUTATED	5	6	6	1	2	0
AMP PEAK 19(5Q35.2) WILD-TYPE	277	44	105	1	44	6

Figure S48. Get High-res Image Gene #18: 'amp_5q35.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'amp_5q35.2' versus 'PATHOLOGY_N_STAGE'

P value = 0.0191 (Fisher's exact test), Q value = 0.22

Table S49. Gene #18: 'amp_5q35.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	225	224
AMP PEAK 19(5Q35.2) MUTATED	13	3
AMP PEAK 19(5Q35.2) WILD-TYPE	212	221

Figure S49. Get High-res Image Gene #18: 'amp_5q35.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_5q35.2' versus 'HISTOLOGICAL_TYPE'

P value = 0.0177 (Fisher's exact test), Q value = 0.22

Table S50. Gene #18: 'amp_5q35.2' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients	OTHER SPECIFY	THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL	THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)	THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
ALL	8	355	100	36
AMP PEAK 19(5Q35.2) MUTATED	0	10	10	0
AMP PEAK 19(5Q35.2) WILD-TYPE	8	345	90	36

Figure S50. Get High-res Image Gene #18: 'amp_5q35.2' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_5q35.2' versus 'EXTRATHYROIDAL_EXTENSION'

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

Table S51. Gene #18: 'amp_5q35.2' versus Clinical Feature #11: 'EXTRATHYROIDAL_EXTENSION'

nPatients	MINIMAL (T3)	MODERATE/ADVANCED (T4A)	NONE	VERY ADVANCED (T4B)
ALL	132	18	330	1
AMP PEAK 19(5Q35.2) MUTATED	3	2	14	1
AMP PEAK 19(5Q35.2) WILD-TYPE	129	16	316	0

Figure S51. Get High-res Image Gene #18: 'amp_5q35.2' versus Clinical Feature #11: 'EXTRATHYROIDAL_EXTENSION'

'amp_5q35.2' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00617 (Wilcoxon-test), Q value = 0.16

Table S52. Gene #18: 'amp_5q35.2' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	385	3.6 (6.0)
AMP PEAK 19(5Q35.2) MUTATED	14	0.9 (2.2)
AMP PEAK 19(5Q35.2) WILD-TYPE	371	3.7 (6.1)

Figure S52. Get High-res Image Gene #18: 'amp_5q35.2' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'amp_5q35.2' versus 'TUMOR_SIZE'

P value = 0.00728 (Wilcoxon-test), Q value = 0.16

Table S53. Gene #18: 'amp_5q35.2' versus Clinical Feature #15: 'TUMOR_SIZE'

	nPatients	Mean (Std.Dev)
ALL	401	3.0 (1.6)
AMP PEAK 19(5Q35.2) MUTATED	19	4.0 (1.8)
AMP PEAK 19(5Q35.2) WILD-TYPE	382	2.9 (1.5)

Figure S53. Get High-res Image Gene #18: 'amp_5q35.2' versus Clinical Feature #15: 'TUMOR_SIZE'

'amp_6p22.3' versus 'Time to Death'

P value = 0.000698 (logrank test), Q value = 0.06

Table S54. Gene #19: 'amp_6p22.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	497	16	0.2 - 169.3 (30.6)
AMP PEAK 20(6P22.3) MUTATED	3	1	30.0 - 34.4 (33.6)
AMP PEAK 20(6P22.3) WILD-TYPE	494	15	0.2 - 169.3 (30.6)

Figure S54. Get High-res Image Gene #19: 'amp_6p22.3' versus Clinical Feature #1: 'Time to Death'

'amp_6p22.2' versus 'Time to Death'

P value = 2.68e-07 (logrank test), Q value = 0.00044

Table S55. Gene #20: 'amp_6p22.2' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	497	16	0.2 - 169.3 (30.6)
AMP PEAK 21(6P22.2) MUTATED	4	2	17.4 - 57.0 (34.0)
AMP PEAK 21(6P22.2) WILD-TYPE	493	14	0.2 - 169.3 (30.6)

Figure S55. Get High-res Image Gene #20: 'amp_6p22.2' versus Clinical Feature #1: 'Time to Death'

'amp_6p22.2' versus 'YEARS_TO_BIRTH'

P value = 0.00456 (Wilcoxon-test), Q value = 0.14

Table S56. Gene #20: 'amp_6p22.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	499	47.3 (15.8)
AMP PEAK 21(6P22.2) MUTATED	4	74.2 (13.3)
AMP PEAK 21(6P22.2) WILD-TYPE	495	47.1 (15.6)

Figure S56. Get High-res Image Gene #20: 'amp_6p22.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_6p21.31' versus 'Time to Death'

P value = 0.00635 (logrank test), Q value = 0.16

Table S57. Gene #21: 'amp_6p21.31' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	497	16	0.2 - 169.3 (30.6)
AMP PEAK 22(6P21.31) MUTATED	3	1	33.6 - 50.2 (34.4)
AMP PEAK 22(6P21.31) WILD-TYPE	494	15	0.2 - 169.3 (30.6)

Figure S57. Get High-res Image Gene #21: 'amp_6p21.31' versus Clinical Feature #1: 'Time to Death'

'amp_6p21.31' versus 'PATHOLOGIC_STAGE'

P value = 0.0121 (Fisher's exact test), Q value = 0.18

Table S58. Gene #21: 'amp_6p21.31' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV	STAGE IVA	STAGE IVC
ALL	282	50	111	2	46	6
AMP PEAK 22(6P21.31) MUTATED	0	1	1	0	0	1
AMP PEAK 22(6P21.31) WILD-TYPE	282	49	110	2	46	5

Figure S58. Get High-res Image Gene #21: 'amp_6p21.31' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'amp_7q11.21' versus 'PATHOLOGIC_STAGE'

P value = 0.0178 (Fisher's exact test), Q value = 0.22

Table S59. Gene #26: 'amp_7q11.21' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV	STAGE IVA	STAGE IVC
ALL	282	50	111	2	46	6
AMP PEAK 27(7Q11.21) MUTATED	9	6	3	1	1	0
AMP PEAK 27(7Q11.21) WILD-TYPE	273	44	108	1	45	6

Figure S59. Get High-res Image Gene #26: 'amp_7q11.21' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'amp_7q11.21' versus 'PATHOLOGY_N_STAGE'

P value = 0.00649 (Fisher's exact test), Q value = 0.16

Table S60. Gene #26: 'amp_7q11.21' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	225	224
AMP PEAK 27(7Q11.21) MUTATED	13	2
AMP PEAK 27(7Q11.21) WILD-TYPE	212	222

Figure S60. Get High-res Image Gene #26: 'amp_7q11.21' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_7q11.21' versus 'EXTRATHYROIDAL_EXTENSION'

P value = 0.00432 (Fisher's exact test), Q value = 0.14

Table S61. Gene #26: 'amp_7q11.21' versus Clinical Feature #11: 'EXTRATHYROIDAL_EXTENSION'

nPatients	MINIMAL (T3)	MODERATE/ADVANCED (T4A)	NONE	VERY ADVANCED (T4B)
ALL	132	18	330	1
AMP PEAK 27(7Q11.21) MUTATED	1	1	16	1
AMP PEAK 27(7Q11.21) WILD-TYPE	131	17	314	0

Figure S61. Get High-res Image Gene #26: 'amp_7q11.21' versus Clinical Feature #11: 'EXTRATHYROIDAL_EXTENSION'

'amp_7q11.21' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00192 (Wilcoxon-test), Q value = 0.11

Table S62. Gene #26: 'amp_7q11.21' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	385	3.6 (6.0)
AMP PEAK 27(7Q11.21) MUTATED	13	0.5 (1.9)
AMP PEAK 27(7Q11.21) WILD-TYPE	372	3.7 (6.1)

Figure S62. Get High-res Image Gene #26: 'amp_7q11.21' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'amp_7q21.11' versus 'YEARS_TO_BIRTH'

P value = 0.0092 (Wilcoxon-test), Q value = 0.17

Table S63. Gene #27: 'amp_7q21.11' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	499	47.3 (15.8)
AMP PEAK 28(7Q21.11) MUTATED	21	55.7 (13.4)
AMP PEAK 28(7Q21.11) WILD-TYPE	478	46.9 (15.8)

Figure S63. Get High-res Image Gene #27: 'amp_7q21.11' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_7q21.11' versus 'PATHOLOGIC_STAGE'

P value = 0.0223 (Fisher's exact test), Q value = 0.23

Table S64. Gene #27: 'amp_7q21.11' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV	STAGE IVA	STAGE IVC
ALL	282	50	111	2	46	6
AMP PEAK 28(7Q21.11) MUTATED	9	6	4	1	1	0
AMP PEAK 28(7Q21.11) WILD-TYPE	273	44	107	1	45	6

Figure S64. Get High-res Image Gene #27: 'amp_7q21.11' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'amp_7q21.11' versus 'PATHOLOGY_N_STAGE'

P value = 0.0191 (Fisher's exact test), Q value = 0.22

Table S65. Gene #27: 'amp_7q21.11' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	225	224
AMP PEAK 28(7Q21.11) MUTATED	13	3
AMP PEAK 28(7Q21.11) WILD-TYPE	212	221

Figure S65. Get High-res Image Gene #27: 'amp_7q21.11' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_7q21.11' versus 'EXTRATHYROIDAL_EXTENSION'

P value = 0.0147 (Fisher's exact test), Q value = 0.2

Table S66. Gene #27: 'amp_7q21.11' versus Clinical Feature #11: 'EXTRATHYROIDAL_EXTENSION'

nPatients	MINIMAL (T3)	MODERATE/ADVANCED (T4A)	NONE	VERY ADVANCED (T4B)
ALL	132	18	330	1
AMP PEAK 28(7Q21.11) MUTATED	2	1	16	1
AMP PEAK 28(7Q21.11) WILD-TYPE	130	17	314	0

Figure S66. Get High-res Image Gene #27: 'amp_7q21.11' versus Clinical Feature #11: 'EXTRATHYROIDAL_EXTENSION'

'amp_7q21.11' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00108 (Wilcoxon-test), Q value = 0.08

Table S67. Gene #27: 'amp_7q21.11' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	385	3.6 (6.0)
AMP PEAK 28(7Q21.11) MUTATED	14	0.5 (1.9)
AMP PEAK 28(7Q21.11) WILD-TYPE	371	3.7 (6.1)

Figure S67. Get High-res Image Gene #27: 'amp_7q21.11' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'amp_7q31.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.0105 (Fisher's exact test), Q value = 0.18

Table S68. Gene #28: 'amp_7q31.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients	OTHER SPECIFY	THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL	THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)	THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
ALL	8	355	100	36
AMP PEAK 29(7Q31.1) MUTATED	0	11	11	0
AMP PEAK 29(7Q31.1) WILD-TYPE	8	344	89	36

Figure S68. Get High-res Image Gene #28: 'amp_7q31.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_7q31.1' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0104 (Wilcoxon-test), Q value = 0.18

Table S69. Gene #28: 'amp_7q31.1' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	385	3.6 (6.0)
AMP PEAK 29(7Q31.1) MUTATED	15	1.1 (2.6)
AMP PEAK 29(7Q31.1) WILD-TYPE	370	3.7 (6.1)

Figure S69. Get High-res Image Gene #28: 'amp_7q31.1' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'amp_7q34' versus 'PATHOLOGY_N_STAGE'

P value = 0.0191 (Fisher's exact test), Q value = 0.22

Table S70. Gene #29: 'amp_7q34' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	225	224
AMP PEAK 30(7Q34) MUTATED	13	3
AMP PEAK 30(7Q34) WILD-TYPE	212	221

Figure S70. Get High-res Image Gene #29: 'amp_7q34' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_7q34' versus 'HISTOLOGICAL_TYPE'

P value = 0.0105 (Fisher's exact test), Q value = 0.18

Table S71. Gene #29: 'amp_7q34' 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	8	355	100	36
AMP PEAK 30(7Q34) MUTATED	0	11	11	0
AMP PEAK 30(7Q34) WILD-TYPE	8	344	89	36

Figure S71. Get High-res Image Gene #29: 'amp_7q34' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_7q34' versus 'EXTRATHYROIDAL_EXTENSION'

P value = 0.0119 (Fisher's exact test), Q value = 0.18

Table S72. Gene #29: 'amp_7q34' versus Clinical Feature #11: 'EXTRATHYROIDAL_EXTENSION'

nPatients	MINIMAL (T3)	MODERATE/ADVANCED (T4A)	NONE	VERY ADVANCED (T4B)
ALL	132	18	330	1
AMP PEAK 30(7Q34) MUTATED	2	1	17	1
AMP PEAK 30(7Q34) WILD-TYPE	130	17	313	0

Figure S72. Get High-res Image Gene #29: 'amp_7q34' versus Clinical Feature #11: 'EXTRATHYROIDAL_EXTENSION'

'amp_7q34' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00562 (Wilcoxon-test), Q value = 0.16

Table S73. Gene #29: 'amp_7q34' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	385	3.6 (6.0)
AMP PEAK 30(7Q34) MUTATED	15	1.3 (3.5)
AMP PEAK 30(7Q34) WILD-TYPE	370	3.7 (6.1)

Figure S73. Get High-res Image Gene #29: 'amp_7q34' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'amp_9q31.1' versus 'TUMOR_SIZE'

P value = 0.0107 (Wilcoxon-test), Q value = 0.18

Table S74. Gene #31: 'amp_9q31.1' versus Clinical Feature #15: 'TUMOR_SIZE'

	nPatients	Mean (Std.Dev)
ALL	401	3.0 (1.6)
AMP PEAK 32(9Q31.1) MUTATED	6	4.3 (0.8)
AMP PEAK 32(9Q31.1) WILD-TYPE	395	2.9 (1.6)

Figure S74. Get High-res Image Gene #31: 'amp_9q31.1' versus Clinical Feature #15: 'TUMOR_SIZE'

'amp_9q34.3' versus 'TUMOR_SIZE'

P value = 0.00874 (Wilcoxon-test), Q value = 0.17

Table S75. Gene #32: 'amp_9q34.3' versus Clinical Feature #15: 'TUMOR_SIZE'

	nPatients	Mean (Std.Dev)
ALL	401	3.0 (1.6)
AMP PEAK 33(9Q34.3) MUTATED	7	4.5 (1.4)
AMP PEAK 33(9Q34.3) WILD-TYPE	394	2.9 (1.6)

Figure S75. Get High-res Image Gene #32: 'amp_9q34.3' versus Clinical Feature #15: 'TUMOR_SIZE'

'amp_10q24.2' versus 'Time to Death'

P value = 0.00835 (logrank test), Q value = 0.17

Table S76. Gene #33: 'amp_10q24.2' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	497	16	0.2 - 169.3 (30.6)
AMP PEAK 34(10Q24.2) MUTATED	3	1	10.7 - 78.6 (33.2)
AMP PEAK 34(10Q24.2) WILD-TYPE	494	15	0.2 - 169.3 (30.6)

Figure S76. Get High-res Image Gene #33: 'amp_10q24.2' versus Clinical Feature #1: 'Time to Death'

'amp_10q24.2' versus 'YEARS_TO_BIRTH'

P value = 0.00952 (Wilcoxon-test), Q value = 0.18

Table S77. Gene #33: 'amp_10q24.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	499	47.3 (15.8)
AMP PEAK 34(10Q24.2) MUTATED	3	74.0 (7.9)
AMP PEAK 34(10Q24.2) WILD-TYPE	496	47.1 (15.7)

Figure S77. Get High-res Image Gene #33: 'amp_10q24.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_10q24.2' versus 'HISTOLOGICAL_TYPE'

P value = 0.0207 (Fisher's exact test), Q value = 0.23

Table S78. Gene #33: 'amp_10q24.2' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients	OTHER SPECIFY	THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL	THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)	THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
ALL	8	355	100	36
AMP PEAK 34(10Q24.2) MUTATED	0	0	3	0
AMP PEAK 34(10Q24.2) WILD-TYPE	8	355	97	36

Figure S78. Get High-res Image Gene #33: 'amp_10q24.2' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_12p11.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.00176 (Fisher's exact test), Q value = 0.11

Table S79. Gene #36: 'amp_12p11.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	225	224
AMP PEAK 37(12P11.1) MUTATED	10	0
AMP PEAK 37(12P11.1) WILD-TYPE	215	224

Figure S79. Get High-res Image Gene #36: 'amp_12p11.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_12p11.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.0024 (Fisher's exact test), Q value = 0.11

Table S80. Gene #36: 'amp_12p11.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients	OTHER SPECIFY	THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL	THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)	THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
ALL	8	355	100	36
AMP PEAK 37(12P11.1) MUTATED	0	6	10	0
AMP PEAK 37(12P11.1) WILD-TYPE	8	349	90	36

Figure S80. Get High-res Image Gene #36: 'amp_12p11.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_12p11.1' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00206 (Wilcoxon-test), Q value = 0.11

Table S81. Gene #36: 'amp_12p11.1' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	385	3.6 (6.0)
AMP PEAK 37(12P11.1) MUTATED	9	0.0 (0.0)
AMP PEAK 37(12P11.1) WILD-TYPE	376	3.7 (6.0)

Figure S81. Get High-res Image Gene #36: 'amp_12p11.1' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'amp_12q21.31' versus 'PATHOLOGY_N_STAGE'

P value = 0.00042 (Fisher's exact test), Q value = 0.057

Table S82. Gene #37: 'amp_12q21.31' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	225	224
AMP PEAK 38(12Q21.31) MUTATED	12	0
AMP PEAK 38(12Q21.31) WILD-TYPE	213	224

Figure S82. Get High-res Image Gene #37: 'amp_12q21.31' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_12q21.31' versus 'HISTOLOGICAL_TYPE'

P value = 0.0183 (Fisher's exact test), Q value = 0.22

Table S83. Gene #37: 'amp_12q21.31' 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	8	355	100	36
AMP PEAK 38(12Q21.31) MUTATED	0	8	9	0
AMP PEAK 38(12Q21.31) WILD-TYPE	8	347	91	36

Figure S83. Get High-res Image Gene #37: 'amp_12q21.31' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_12q21.31' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000634 (Wilcoxon-test), Q value = 0.06

Table S84. Gene #37: 'amp_12q21.31' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	385	3.6 (6.0)
AMP PEAK 38(12Q21.31) MUTATED	11	0.0 (0.0)
AMP PEAK 38(12Q21.31) WILD-TYPE	374	3.7 (6.0)

Figure S84. Get High-res Image Gene #37: 'amp_12q21.31' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'amp_12q23.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.00572 (Fisher's exact test), Q value = 0.16

Table S85. Gene #38: 'amp_12q23.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	225	224
AMP PEAK 39(12Q23.1) MUTATED	11	1
AMP PEAK 39(12Q23.1) WILD-TYPE	214	223

Figure S85. Get High-res Image Gene #38: 'amp_12q23.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_12q23.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.0179 (Fisher's exact test), Q value = 0.22

Table S86. Gene #38: 'amp_12q23.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients	OTHER SPECIFY	THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL	THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)	THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
ALL	8	355	100	36
AMP PEAK 39(12Q23.1) MUTATED	0	8	9	0
AMP PEAK 39(12Q23.1) WILD-TYPE	8	347	91	36

Figure S86. Get High-res Image Gene #38: 'amp_12q23.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_12q23.1' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00611 (Wilcoxon-test), Q value = 0.16

Table S87. Gene #38: 'amp_12q23.1' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	385	3.6 (6.0)
AMP PEAK 39(12Q23.1) MUTATED	11	0.6 (2.1)
AMP PEAK 39(12Q23.1) WILD-TYPE	374	3.7 (6.0)

Figure S87. Get High-res Image Gene #38: 'amp_12q23.1' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'amp_13q34' versus 'HISTOLOGICAL_TYPE'

P value = 0.0112 (Fisher's exact test), Q value = 0.18

Table S88. Gene #40: 'amp_13q34' 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	8	355	100	36
AMP PEAK 41(13Q34) MUTATED	1	2	4	0
AMP PEAK 41(13Q34) WILD-TYPE	7	353	96	36

Figure S88. Get High-res Image Gene #40: 'amp_13q34' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_14q12' versus 'PATHOLOGIC_STAGE'

P value = 0.0212 (Fisher's exact test), Q value = 0.23

Table S89. Gene #41: 'amp_14q12' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV	STAGE IVA	STAGE IVC
ALL	282	50	111	2	46	6
AMP PEAK 42(14Q12) MUTATED	3	5	4	0	1	0
AMP PEAK 42(14Q12) WILD-TYPE	279	45	107	2	45	6

Figure S89. Get High-res Image Gene #41: 'amp_14q12' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'amp_14q32.31' versus 'PATHOLOGIC_STAGE'

P value = 0.00312 (Fisher's exact test), Q value = 0.12

Table S90. Gene #42: 'amp_14q32.31' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV	STAGE IVA	STAGE IVC
ALL	282	50	111	2	46	6
AMP PEAK 43(14Q32.31) MUTATED	2	5	6	0	0	0
AMP PEAK 43(14Q32.31) WILD-TYPE	280	45	105	2	46	6

Figure S90. Get High-res Image Gene #42: 'amp_14q32.31' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'amp_14q32.31' versus 'PATHOLOGY_N_STAGE'

P value = 0.0201 (Fisher's exact test), Q value = 0.22

Table S91. Gene #42: 'amp_14q32.31' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	225	224
AMP PEAK 43(14Q32.31) MUTATED	9	1
AMP PEAK 43(14Q32.31) WILD-TYPE	216	223

Figure S91. Get High-res Image Gene #42: 'amp_14q32.31' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_14q32.31' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0174 (Wilcoxon-test), Q value = 0.22

Table S92. Gene #42: 'amp_14q32.31' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	385	3.6 (6.0)
AMP PEAK 43(14Q32.31) MUTATED	9	0.7 (2.0)
AMP PEAK 43(14Q32.31) WILD-TYPE	376	3.6 (6.0)

Figure S92. Get High-res Image Gene #42: 'amp_14q32.31' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'amp_18q22.3' versus 'PATHOLOGY_N_STAGE'

P value = 0.0149 (Fisher's exact test), Q value = 0.2

Table S93. Gene #45: 'amp_18q22.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	225	224
AMP PEAK 48(18Q22.3) MUTATED	7	0
AMP PEAK 48(18Q22.3) WILD-TYPE	218	224

Figure S93. Get High-res Image Gene #45: 'amp_18q22.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_18q22.3' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0122 (Wilcoxon-test), Q value = 0.18

Table S94. Gene #45: 'amp_18q22.3' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	385	3.6 (6.0)
AMP PEAK 48(18Q22.3) MUTATED	6	0.0 (0.0)
AMP PEAK 48(18Q22.3) WILD-TYPE	379	3.6 (6.0)

Figure S94. Get High-res Image Gene #45: 'amp_18q22.3' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'amp_19p13.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.0104 (Fisher's exact test), Q value = 0.18

Table S95. Gene #46: 'amp_19p13.3' 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	8	355	100	36
AMP PEAK 49(19P13.3) MUTATED	0	2	6	0
AMP PEAK 49(19P13.3) WILD-TYPE	8	353	94	36

Figure S95. Get High-res Image Gene #46: 'amp_19p13.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_20p13' versus 'PATHOLOGIC_STAGE'

P value = 0.0145 (Fisher's exact test), Q value = 0.2

Table S96. Gene #47: 'amp_20p13' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV	STAGE IVA	STAGE IVC
ALL	282	50	111	2	46	6
AMP PEAK 50(20P13) MUTATED	5	4	4	1	0	0
AMP PEAK 50(20P13) WILD-TYPE	277	46	107	1	46	6

Figure S96. Get High-res Image Gene #47: 'amp_20p13' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'amp_20p13' versus 'HISTOLOGICAL_TYPE'

P value = 0.017 (Fisher's exact test), Q value = 0.21

Table S97. Gene #47: 'amp_20p13' 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	8	355	100	36
AMP PEAK 50(20P13) MUTATED	0	6	8	0
AMP PEAK 50(20P13) WILD-TYPE	8	349	92	36

Figure S97. Get High-res Image Gene #47: 'amp_20p13' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_20p13' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00371 (Wilcoxon-test), Q value = 0.12

Table S98. Gene #47: 'amp_20p13' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	385	3.6 (6.0)
AMP PEAK 50(20P13) MUTATED	8	0.0 (0.0)
AMP PEAK 50(20P13) WILD-TYPE	377	3.6 (6.0)

Figure S98. Get High-res Image Gene #47: 'amp_20p13' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'amp_20q13.11' versus 'PATHOLOGY_N_STAGE'

P value = 0.0201 (Fisher's exact test), Q value = 0.22

Table S99. Gene #48: 'amp_20q13.11' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	225	224
AMP PEAK 51(20Q13.11) MUTATED	9	1
AMP PEAK 51(20Q13.11) WILD-TYPE	216	223

Figure S99. Get High-res Image Gene #48: 'amp_20q13.11' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_20q13.11' versus 'HISTOLOGICAL_TYPE'

P value = 0.00358 (Fisher's exact test), Q value = 0.12

Table S100. Gene #48: 'amp_20q13.11' 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	8	355	100	36
AMP PEAK 51(20Q13.11) MUTATED	0	5	9	0
AMP PEAK 51(20Q13.11) WILD-TYPE	8	350	91	36

Figure S100. Get High-res Image Gene #48: 'amp_20q13.11' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_20q13.11' versus 'EXTRATHYROIDAL_EXTENSION'

P value = 0.0102 (Fisher's exact test), Q value = 0.18

Table S101. Gene #48: 'amp_20q13.11' versus Clinical Feature #11: 'EXTRATHYROIDAL_EXTENSION'

nPatients	MINIMAL (T3)	MODERATE/ADVANCED (T4A)	NONE	VERY ADVANCED (T4B)
ALL	132	18	330	1
AMP PEAK 51(20Q13.11) MUTATED	1	0	12	1
AMP PEAK 51(20Q13.11) WILD-TYPE	131	18	318	0

Figure S101. Get High-res Image Gene #48: 'amp_20q13.11' versus Clinical Feature #11: 'EXTRATHYROIDAL_EXTENSION'

'amp_20q13.11' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00206 (Wilcoxon-test), Q value = 0.11

Table S102. Gene #48: 'amp_20q13.11' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	385	3.6 (6.0)
AMP PEAK 51(20Q13.11) MUTATED	9	0.0 (0.0)
AMP PEAK 51(20Q13.11) WILD-TYPE	376	3.7 (6.0)

Figure S102. Get High-res Image Gene #48: 'amp_20q13.11' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'amp_20q13.2' versus 'YEARS_TO_BIRTH'

P value = 0.0223 (Wilcoxon-test), Q value = 0.23

Table S103. Gene #49: 'amp_20q13.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	499	47.3 (15.8)
AMP PEAK 52(20Q13.2) MUTATED	14	56.6 (14.7)
AMP PEAK 52(20Q13.2) WILD-TYPE	485	47.0 (15.7)

Figure S103. Get High-res Image Gene #49: 'amp_20q13.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_20q13.2' versus 'HISTOLOGICAL_TYPE'

P value = 0.00376 (Fisher's exact test), Q value = 0.12

Table S104. Gene #49: 'amp_20q13.2' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients	OTHER SPECIFY	THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL	THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)	THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
ALL	8	355	100	36
AMP PEAK 52(20Q13.2) MUTATED	0	5	9	0
AMP PEAK 52(20Q13.2) WILD-TYPE	8	350	91	36

Figure S104. Get High-res Image Gene #49: 'amp_20q13.2' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_20q13.2' versus 'EXTRATHYROIDAL_EXTENSION'

P value = 0.0097 (Fisher's exact test), Q value = 0.18

Table S105. Gene #49: 'amp_20q13.2' versus Clinical Feature #11: 'EXTRATHYROIDAL_EXTENSION'

nPatients	MINIMAL (T3)	MODERATE/ADVANCED (T4A)	NONE	VERY ADVANCED (T4B)
ALL	132	18	330	1
AMP PEAK 52(20Q13.2) MUTATED	1	0	12	1
AMP PEAK 52(20Q13.2) WILD-TYPE	131	18	318	0

Figure S105. Get High-res Image Gene #49: 'amp_20q13.2' versus Clinical Feature #11: 'EXTRATHYROIDAL_EXTENSION'

'amp_20q13.2' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0223 (Wilcoxon-test), Q value = 0.23

Table S106. Gene #49: 'amp_20q13.2' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	385	3.6 (6.0)
AMP PEAK 52(20Q13.2) MUTATED	9	1.0 (3.0)
AMP PEAK 52(20Q13.2) WILD-TYPE	376	3.6 (6.0)

Figure S106. Get High-res Image Gene #49: 'amp_20q13.2' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'amp_20q13.2' versus 'PATHOLOGIC_STAGE'

P value = 0.00735 (Fisher's exact test), Q value = 0.16

Table S107. Gene #50: 'amp_20q13.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV	STAGE IVA	STAGE IVC
ALL	282	50	111	2	46	6
AMP PEAK 53(20Q13.2) MUTATED	4	4	4	1	0	0
AMP PEAK 53(20Q13.2) WILD-TYPE	278	46	107	1	46	6

Figure S107. Get High-res Image Gene #50: 'amp_20q13.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'amp_20q13.2' versus 'HISTOLOGICAL_TYPE'

P value = 0.00474 (Fisher's exact test), Q value = 0.14

Table S108. Gene #50: 'amp_20q13.2' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients	OTHER SPECIFY	THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL	THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)	THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
ALL	8	355	100	36
AMP PEAK 53(20Q13.2) MUTATED	0	4	8	1
AMP PEAK 53(20Q13.2) WILD-TYPE	8	351	92	35

Figure S108. Get High-res Image Gene #50: 'amp_20q13.2' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_20q13.2' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0239 (Wilcoxon-test), Q value = 0.25

Table S109. Gene #50: 'amp_20q13.2' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	385	3.6 (6.0)
AMP PEAK 53(20Q13.2) MUTATED	8	0.5 (1.4)
AMP PEAK 53(20Q13.2) WILD-TYPE	377	3.6 (6.0)

Figure S109. Get High-res Image Gene #50: 'amp_20q13.2' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'amp_22q11.21' versus 'RESIDUAL_TUMOR'

P value = 0.0129 (Fisher's exact test), Q value = 0.19

Table S110. Gene #52: 'amp_22q11.21' versus Clinical Feature #12: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	383	51	4	30
AMP PEAK 55(22Q11.21) MUTATED	2	2	0	2
AMP PEAK 55(22Q11.21) WILD-TYPE	381	49	4	28

Figure S110. Get High-res Image Gene #52: 'amp_22q11.21' versus Clinical Feature #12: 'RESIDUAL_TUMOR'

'amp_xp22.12' versus 'YEARS_TO_BIRTH'

P value = 0.0131 (Wilcoxon-test), Q value = 0.19

Table S111. Gene #53: 'amp_xp22.12' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	499	47.3 (15.8)
AMP PEAK 56(XP22.12) MUTATED	10	58.5 (10.2)
AMP PEAK 56(XP22.12) WILD-TYPE	489	47.0 (15.8)

Figure S111. Get High-res Image Gene #53: 'amp_xp22.12' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_xp22.12' versus 'PATHOLOGIC_STAGE'

P value = 0.00252 (Fisher's exact test), Q value = 0.11

Table S112. Gene #53: 'amp_xp22.12' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV	STAGE IVA	STAGE IVC
ALL	282	50	111	2	46	6
AMP PEAK 56(XP22.12) MUTATED	2	4	2	1	1	0
AMP PEAK 56(XP22.12) WILD-TYPE	280	46	109	1	45	6

Figure S112. Get High-res Image Gene #53: 'amp_xp22.12' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'amp_xp22.12' versus 'RESIDUAL_TUMOR'

P value = 0.0153 (Fisher's exact test), Q value = 0.2

Table S113. Gene #53: 'amp_xp22.12' versus Clinical Feature #12: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	383	51	4	30
AMP PEAK 56(XP22.12) MUTATED	5	2	0	3
AMP PEAK 56(XP22.12) WILD-TYPE	378	49	4	27

Figure S113. Get High-res Image Gene #53: 'amp_xp22.12' versus Clinical Feature #12: 'RESIDUAL_TUMOR'

'amp_xp11.4' versus 'YEARS_TO_BIRTH'

P value = 0.00502 (Wilcoxon-test), Q value = 0.15

Table S114. Gene #54: 'amp_xp11.4' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	499	47.3 (15.8)
AMP PEAK 57(XP11.4) MUTATED	9	61.2 (10.9)
AMP PEAK 57(XP11.4) WILD-TYPE	490	47.0 (15.7)

Figure S114. Get High-res Image Gene #54: 'amp_xp11.4' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_xp11.4' versus 'PATHOLOGIC_STAGE'

P value = 0.00754 (Fisher's exact test), Q value = 0.16

Table S115. Gene #54: 'amp_xp11.4' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV	STAGE IVA	STAGE IVC
ALL	282	50	111	2	46	6
AMP PEAK 57(XP11.4) MUTATED	2	3	2	1	1	0
AMP PEAK 57(XP11.4) WILD-TYPE	280	47	109	1	45	6

Figure S115. Get High-res Image Gene #54: 'amp_xp11.4' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'amp_xp11.4' versus 'EXTRATHYROIDAL_EXTENSION'

P value = 0.0192 (Fisher's exact test), Q value = 0.22

Table S116. Gene #54: 'amp_xp11.4' versus Clinical Feature #11: 'EXTRATHYROIDAL_EXTENSION'

nPatients	MINIMAL (T3)	MODERATE/ADVANCED (T4A)	NONE	VERY ADVANCED (T4B)
ALL	132	18	330	1
AMP PEAK 57(XP11.4) MUTATED	1	0	7	1
AMP PEAK 57(XP11.4) WILD-TYPE	131	18	323	0

Figure S116. Get High-res Image Gene #54: 'amp_xp11.4' versus Clinical Feature #11: 'EXTRATHYROIDAL_EXTENSION'

'amp_xq21.2' versus 'EXTRATHYROIDAL_EXTENSION'

P value = 0.00918 (Fisher's exact test), Q value = 0.17

Table S117. Gene #57: 'amp_xq21.2' versus Clinical Feature #11: 'EXTRATHYROIDAL_EXTENSION'

nPatients	MINIMAL (T3)	MODERATE/ADVANCED (T4A)	NONE	VERY ADVANCED (T4B)
ALL	132	18	330	1
AMP PEAK 60(XQ21.2) MUTATED	1	1	6	1
AMP PEAK 60(XQ21.2) WILD-TYPE	131	17	324	0

Figure S117. Get High-res Image Gene #57: 'amp_xq21.2' versus Clinical Feature #11: 'EXTRATHYROIDAL_EXTENSION'

'amp_xq22.3' versus 'GENDER'

P value = 0.0147 (Fisher's exact test), Q value = 0.2

Table S118. Gene #58: 'amp_xq22.3' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	365	134
AMP PEAK 61(XQ22.3) MUTATED	15	0
AMP PEAK 61(XQ22.3) WILD-TYPE	350	134

Figure S118. Get High-res Image Gene #58: 'amp_xq22.3' versus Clinical Feature #7: 'GENDER'

'amp_xq22.3' versus 'EXTRATHYROIDAL_EXTENSION'

P value = 0.0101 (Fisher's exact test), Q value = 0.18

Table S119. Gene #58: 'amp_xq22.3' versus Clinical Feature #11: 'EXTRATHYROIDAL_EXTENSION'

nPatients	MINIMAL (T3)	MODERATE/ADVANCED (T4A)	NONE	VERY ADVANCED (T4B)
ALL	132	18	330	1
AMP PEAK 61(XQ22.3) MUTATED	1	0	13	1
AMP PEAK 61(XQ22.3) WILD-TYPE	131	18	317	0

Figure S119. Get High-res Image Gene #58: 'amp_xq22.3' versus Clinical Feature #11: 'EXTRATHYROIDAL_EXTENSION'

'amp_xq23' versus 'EXTRATHYROIDAL_EXTENSION'

P value = 0.0194 (Fisher's exact test), Q value = 0.22

Table S120. Gene #59: 'amp_xq23' versus Clinical Feature #11: 'EXTRATHYROIDAL_EXTENSION'

nPatients	MINIMAL (T3)	MODERATE/ADVANCED (T4A)	NONE	VERY ADVANCED (T4B)
ALL	132	18	330	1
AMP PEAK 62(XQ23) MUTATED	1	0	7	1
AMP PEAK 62(XQ23) WILD-TYPE	131	18	323	0

Figure S120. Get High-res Image Gene #59: 'amp_xq23' versus Clinical Feature #11: 'EXTRATHYROIDAL_EXTENSION'

'amp_xq28' versus 'YEARS_TO_BIRTH'

P value = 0.0205 (Wilcoxon-test), Q value = 0.22

Table S121. Gene #62: 'amp_xq28' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	499	47.3 (15.8)
AMP PEAK 65(XQ28) MUTATED	10	59.4 (16.2)
AMP PEAK 65(XQ28) WILD-TYPE	489	47.0 (15.7)

Figure S121. Get High-res Image Gene #62: 'amp_xq28' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_xq28' versus 'EXTRATHYROIDAL_EXTENSION'

P value = 0.00984 (Fisher's exact test), Q value = 0.18

Table S122. Gene #62: 'amp_xq28' versus Clinical Feature #11: 'EXTRATHYROIDAL_EXTENSION'

nPatients	MINIMAL (T3)	MODERATE/ADVANCED (T4A)	NONE	VERY ADVANCED (T4B)
ALL	132	18	330	1
AMP PEAK 65(XQ28) MUTATED	1	1	7	1
AMP PEAK 65(XQ28) WILD-TYPE	131	17	323	0

Figure S122. Get High-res Image Gene #62: 'amp_xq28' versus Clinical Feature #11: 'EXTRATHYROIDAL_EXTENSION'

'del_2p23.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.0201 (Fisher's exact test), Q value = 0.22

Table S123. Gene #65: 'del_2p23.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	225	224
DEL PEAK 3(2P23.1) MUTATED	9	1
DEL PEAK 3(2P23.1) WILD-TYPE	216	223

Figure S123. Get High-res Image Gene #65: 'del_2p23.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_2p23.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.00303 (Fisher's exact test), Q value = 0.12

Table S124. Gene #65: 'del_2p23.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients	OTHER SPECIFY	THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL	THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)	THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
ALL	8	355	100	36
DEL PEAK 3(2P23.1) MUTATED	1	4	7	0
DEL PEAK 3(2P23.1) WILD-TYPE	7	351	93	36

Figure S124. Get High-res Image Gene #65: 'del_2p23.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_2p23.1' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0112 (Wilcoxon-test), Q value = 0.18

Table S125. Gene #65: 'del_2p23.1' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	385	3.6 (6.0)
DEL PEAK 3(2P23.1) MUTATED	9	0.3 (1.0)
DEL PEAK 3(2P23.1) WILD-TYPE	376	3.6 (6.0)

Figure S125. Get High-res Image Gene #65: 'del_2p23.1' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'del_2q22.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.0149 (Fisher's exact test), Q value = 0.2

Table S126. Gene #66: 'del_2q22.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	225	224
DEL PEAK 4(2Q22.1) MUTATED	7	0
DEL PEAK 4(2Q22.1) WILD-TYPE	218	224

Figure S126. Get High-res Image Gene #66: 'del_2q22.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_2q22.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.00519 (Fisher's exact test), Q value = 0.15

Table S127. Gene #66: 'del_2q22.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients	OTHER SPECIFY	THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL	THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)	THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
ALL	8	355	100	36
DEL PEAK 4(2Q22.1) MUTATED	0	3	7	0
DEL PEAK 4(2Q22.1) WILD-TYPE	8	352	93	36

Figure S127. Get High-res Image Gene #66: 'del_2q22.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_2q22.1' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00672 (Wilcoxon-test), Q value = 0.16

Table S128. Gene #66: 'del_2q22.1' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	385	3.6 (6.0)
DEL PEAK 4(2Q22.1) MUTATED	7	0.0 (0.0)
DEL PEAK 4(2Q22.1) WILD-TYPE	378	3.6 (6.0)

Figure S128. Get High-res Image Gene #66: 'del_2q22.1' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'del_2q37.3' versus 'PATHOLOGIC_STAGE'

P value = 0.0123 (Fisher's exact test), Q value = 0.18

Table S129. Gene #67: 'del_2q37.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV	STAGE IVA	STAGE IVC
ALL	282	50	111	2	46	6
DEL PEAK 5(2Q37.3) MUTATED	4	6	2	0	1	0
DEL PEAK 5(2Q37.3) WILD-TYPE	278	44	109	2	45	6

Figure S129. Get High-res Image Gene #67: 'del_2q37.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_2q37.3' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0158 (Wilcoxon-test), Q value = 0.21

Table S130. Gene #67: 'del_2q37.3' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	385	3.6 (6.0)
DEL PEAK 5(2Q37.3) MUTATED	8	0.2 (0.7)
DEL PEAK 5(2Q37.3) WILD-TYPE	377	3.6 (6.0)

Figure S130. Get High-res Image Gene #67: 'del_2q37.3' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'del_6q22.31' versus 'Time to Death'

P value = 0.00235 (logrank test), Q value = 0.11

Table S131. Gene #70: 'del_6q22.31' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	497	16	0.2 - 169.3 (30.6)
DEL PEAK 11(6Q22.31) MUTATED	6	2	7.8 - 123.3 (43.9)
DEL PEAK 11(6Q22.31) WILD-TYPE	491	14	0.2 - 169.3 (30.6)

Figure S131. Get High-res Image Gene #70: 'del_6q22.31' versus Clinical Feature #1: 'Time to Death'

'del_6q22.31' versus 'TUMOR_SIZE'

P value = 0.00914 (Wilcoxon-test), Q value = 0.17

Table S132. Gene #70: 'del_6q22.31' versus Clinical Feature #15: 'TUMOR_SIZE'

	nPatients	Mean (Std.Dev)
ALL	401	3.0 (1.6)
DEL PEAK 11(6Q22.31) MUTATED	6	4.6 (1.2)
DEL PEAK 11(6Q22.31) WILD-TYPE	395	2.9 (1.6)

Figure S132. Get High-res Image Gene #70: 'del_6q22.31' versus Clinical Feature #15: 'TUMOR_SIZE'

'del_8q24.22' versus 'GENDER'

P value = 0.017 (Fisher's exact test), Q value = 0.21

Table S133. Gene #75: 'del_8q24.22' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	365	134
DEL PEAK 17(8Q24.22) MUTATED	2	5
DEL PEAK 17(8Q24.22) WILD-TYPE	363	129

Figure S133. Get High-res Image Gene #75: 'del_8q24.22' versus Clinical Feature #7: 'GENDER'

'del_9p21.3' versus 'YEARS_TO_BIRTH'

P value = 0.00966 (Wilcoxon-test), Q value = 0.18

Table S134. Gene #76: 'del_9p21.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	499	47.3 (15.8)
DEL PEAK 18(9P21.3) MUTATED	20	56.8 (16.0)
DEL PEAK 18(9P21.3) WILD-TYPE	479	46.9 (15.6)

Figure S134. Get High-res Image Gene #76: 'del_9p21.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_9p21.3' versus 'PATHOLOGIC_STAGE'

P value = 0.00024 (Fisher's exact test), Q value = 0.036

Table S135. Gene #76: 'del_9p21.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV	STAGE IVA	STAGE IVC
ALL	282	50	111	2	46	6
DEL PEAK 18(9P21.3) MUTATED	7	5	4	2	1	1
DEL PEAK 18(9P21.3) WILD-TYPE	275	45	107	0	45	5

Figure S135. Get High-res Image Gene #76: 'del_9p21.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_9q22.33' versus 'YEARS_TO_BIRTH'

P value = 0.000623 (Wilcoxon-test), Q value = 0.06

Table S136. Gene #77: 'del_9q22.33' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	499	47.3 (15.8)
DEL PEAK 19(9Q22.33) MUTATED	27	59.2 (19.0)
DEL PEAK 19(9Q22.33) WILD-TYPE	472	46.6 (15.3)

Figure S136. Get High-res Image Gene #77: 'del_9q22.33' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_9q22.33' versus 'PATHOLOGIC_STAGE'

P value = 0.00055 (Fisher's exact test), Q value = 0.06

Table S137. Gene #77: 'del_9q22.33' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV	STAGE IVA	STAGE IVC
ALL	282	50	111	2	46	6
DEL PEAK 19(9Q22.33) MUTATED	10	5	4	2	5	1
DEL PEAK 19(9Q22.33) WILD-TYPE	272	45	107	0	41	5

Figure S137. Get High-res Image Gene #77: 'del_9q22.33' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_9q22.33' versus 'TUMOR_SIZE'

P value = 0.0189 (Wilcoxon-test), Q value = 0.22

Table S138. Gene #77: 'del_9q22.33' versus Clinical Feature #15: 'TUMOR_SIZE'

	nPatients	Mean (Std.Dev)
ALL	401	3.0 (1.6)
DEL PEAK 19(9Q22.33) MUTATED	23	3.8 (1.9)
DEL PEAK 19(9Q22.33) WILD-TYPE	378	2.9 (1.5)

Figure S138. Get High-res Image Gene #77: 'del_9q22.33' versus Clinical Feature #15: 'TUMOR_SIZE'

'del_10p12.31' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0224 (Wilcoxon-test), Q value = 0.23

Table S139. Gene #78: 'del_10p12.31' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	385	3.6 (6.0)
DEL PEAK 20(10P12.31) MUTATED	5	0.0 (0.0)
DEL PEAK 20(10P12.31) WILD-TYPE	380	3.6 (6.0)

Figure S139. Get High-res Image Gene #78: 'del_10p12.31' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'del_10q23.31' versus 'PATHOLOGY_N_STAGE'

P value = 0.0201 (Fisher's exact test), Q value = 0.22

Table S140. Gene #80: 'del_10q23.31' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	225	224
DEL PEAK 22(10Q23.31) MUTATED	9	1
DEL PEAK 22(10Q23.31) WILD-TYPE	216	223

Figure S140. Get High-res Image Gene #80: 'del_10q23.31' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_10q23.31' versus 'TUMOR_SIZE'

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

Table S141. Gene #80: 'del_10q23.31' versus Clinical Feature #15: 'TUMOR_SIZE'

	nPatients	Mean (Std.Dev)
ALL	401	3.0 (1.6)
DEL PEAK 22(10Q23.31) MUTATED	9	4.6 (1.5)
DEL PEAK 22(10Q23.31) WILD-TYPE	392	2.9 (1.6)

Figure S141. Get High-res Image Gene #80: 'del_10q23.31' versus Clinical Feature #15: 'TUMOR_SIZE'

'del_11p15.1' versus 'Time to Death'

P value = 0.0193 (logrank test), Q value = 0.22

Table S142. Gene #81: 'del_11p15.1' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	497	16	0.2 - 169.3 (30.6)
DEL PEAK 23(11P15.1) MUTATED	7	1	7.8 - 49.5 (23.9)
DEL PEAK 23(11P15.1) WILD-TYPE	490	15	0.2 - 169.3 (30.6)

Figure S142. Get High-res Image Gene #81: 'del_11p15.1' versus Clinical Feature #1: 'Time to Death'

'del_11p15.1' versus 'YEARS_TO_BIRTH'

P value = 0.000675 (Wilcoxon-test), Q value = 0.06

Table S143. Gene #81: 'del_11p15.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	499	47.3 (15.8)
DEL PEAK 23(11P15.1) MUTATED	7	68.1 (8.7)
DEL PEAK 23(11P15.1) WILD-TYPE	492	47.0 (15.6)

Figure S143. Get High-res Image Gene #81: 'del_11p15.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_11p15.1' versus 'PATHOLOGIC_STAGE'

P value = 0.0055 (Fisher's exact test), Q value = 0.15

Table S144. Gene #81: 'del_11p15.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV	STAGE IVA	STAGE IVC
ALL	282	50	111	2	46	6
DEL PEAK 23(11P15.1) MUTATED	1	1	4	1	0	0
DEL PEAK 23(11P15.1) WILD-TYPE	281	49	107	1	46	6

Figure S144. Get High-res Image Gene #81: 'del_11p15.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_11p15.1' versus 'GENDER'

P value = 0.017 (Fisher's exact test), Q value = 0.21

Table S145. Gene #81: 'del_11p15.1' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	365	134
DEL PEAK 23(11P15.1) MUTATED	2	5
DEL PEAK 23(11P15.1) WILD-TYPE	363	129

Figure S145. Get High-res Image Gene #81: 'del_11p15.1' versus Clinical Feature #7: 'GENDER'

'del_11p15.1' versus 'TUMOR_SIZE'

P value = 0.00751 (Wilcoxon-test), Q value = 0.16

Table S146. Gene #81: 'del_11p15.1' versus Clinical Feature #15: 'TUMOR_SIZE'

	nPatients	Mean (Std.Dev)
ALL	401	3.0 (1.6)
DEL PEAK 23(11P15.1) MUTATED	7	4.9 (1.9)
DEL PEAK 23(11P15.1) WILD-TYPE	394	2.9 (1.6)

Figure S146. Get High-res Image Gene #81: 'del_11p15.1' versus Clinical Feature #15: 'TUMOR_SIZE'

'del_13q12.13' versus 'YEARS_TO_BIRTH'

P value = 0.00677 (Wilcoxon-test), Q value = 0.16

Table S147. Gene #82: 'del_13q12.13' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	499	47.3 (15.8)
DEL PEAK 24(13Q12.13) MUTATED	18	58.1 (16.5)
DEL PEAK 24(13Q12.13) WILD-TYPE	481	46.9 (15.6)

Figure S147. Get High-res Image Gene #82: 'del_13q12.13' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_13q12.13' versus 'RADIATION_EXPOSURE'

P value = 0.00275 (Fisher's exact test), Q value = 0.11

Table S148. Gene #82: 'del_13q12.13' versus Clinical Feature #10: 'RADIATION_EXPOSURE'

nPatients	NO	YES
ALL	420	17
DEL PEAK 24(13Q12.13) MUTATED	13	4
DEL PEAK 24(13Q12.13) WILD-TYPE	407	13

Figure S148. Get High-res Image Gene #82: 'del_13q12.13' versus Clinical Feature #10: 'RADIATION_EXPOSURE'

'del_13q22.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.0191 (Fisher's exact test), Q value = 0.22

Table S149. Gene #83: 'del_13q22.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	225	224
DEL PEAK 25(13Q22.1) MUTATED	13	3
DEL PEAK 25(13Q22.1) WILD-TYPE	212	221

Figure S149. Get High-res Image Gene #83: 'del_13q22.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_13q22.1' versus 'RADIATION_EXPOSURE'

P value = 0.00275 (Fisher's exact test), Q value = 0.11

Table S150. Gene #83: 'del_13q22.1' versus Clinical Feature #10: 'RADIATION_EXPOSURE'

nPatients	NO	YES
ALL	420	17
DEL PEAK 25(13Q22.1) MUTATED	13	4
DEL PEAK 25(13Q22.1) WILD-TYPE	407	13

Figure S150. Get High-res Image Gene #83: 'del_13q22.1' versus Clinical Feature #10: 'RADIATION_EXPOSURE'

'del_16q23.3' versus 'PATHOLOGIC_STAGE'

P value = 0.00219 (Fisher's exact test), Q value = 0.11

Table S151. Gene #85: 'del_16q23.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV	STAGE IVA	STAGE IVC
ALL	282	50	111	2	46	6
DEL PEAK 29(16Q23.3) MUTATED	0	0	3	0	2	1
DEL PEAK 29(16Q23.3) WILD-TYPE	282	50	108	2	44	5

Figure S151. Get High-res Image Gene #85: 'del_16q23.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_16q23.3' versus 'PATHOLOGY_T_STAGE'

P value = 0.0159 (Fisher's exact test), Q value = 0.21

Table S152. Gene #85: 'del_16q23.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	142	165	167	23
DEL PEAK 29(16Q23.3) MUTATED	0	1	3	2
DEL PEAK 29(16Q23.3) WILD-TYPE	142	164	164	21

Figure S152. Get High-res Image Gene #85: 'del_16q23.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_17p13.1' versus 'TUMOR_SIZE'

P value = 0.0141 (Wilcoxon-test), Q value = 0.2

Table S153. Gene #86: 'del_17p13.1' versus Clinical Feature #15: 'TUMOR_SIZE'

	nPatients	Mean (Std.Dev)
ALL	401	3.0 (1.6)
DEL PEAK 30(17P13.1) MUTATED	7	4.5 (1.6)
DEL PEAK 30(17P13.1) WILD-TYPE	394	2.9 (1.6)

Figure S153. Get High-res Image Gene #86: 'del_17p13.1' versus Clinical Feature #15: 'TUMOR_SIZE'

'del_19p13.2' versus 'TUMOR_SIZE'

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

Table S154. Gene #88: 'del_19p13.2' versus Clinical Feature #15: 'TUMOR_SIZE'

	nPatients	Mean (Std.Dev)
ALL	401	3.0 (1.6)
DEL PEAK 32(19P13.2) MUTATED	4	5.8 (0.6)
DEL PEAK 32(19P13.2) WILD-TYPE	397	2.9 (1.6)

Figure S154. Get High-res Image Gene #88: 'del_19p13.2' versus Clinical Feature #15: 'TUMOR_SIZE'

'del_19p13.12' versus 'TUMOR_SIZE'

P value = 0.00769 (Wilcoxon-test), Q value = 0.16

Table S155. Gene #89: 'del_19p13.12' versus Clinical Feature #15: 'TUMOR_SIZE'

	nPatients	Mean (Std.Dev)
ALL	401	3.0 (1.6)
DEL PEAK 33(19P13.12) MUTATED	5	5.2 (1.6)
DEL PEAK 33(19P13.12) WILD-TYPE	396	2.9 (1.6)

Figure S155. Get High-res Image Gene #89: 'del_19p13.12' versus Clinical Feature #15: 'TUMOR_SIZE'

'del_21q21.1' versus 'PATHOLOGIC_STAGE'

P value = 0.00675 (Fisher's exact test), Q value = 0.16

Table S156. Gene #90: 'del_21q21.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV	STAGE IVA	STAGE IVC
ALL	282	50	111	2	46	6
DEL PEAK 36(21Q21.1) MUTATED	1	4	2	0	2	0
DEL PEAK 36(21Q21.1) WILD-TYPE	281	46	109	2	44	6

Figure S156. Get High-res Image Gene #90: 'del_21q21.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_xq23' versus 'PATHOLOGIC_STAGE'

P value = 0.00094 (Fisher's exact test), Q value = 0.077

Table S157. Gene #95: 'del_xq23' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV	STAGE IVA	STAGE IVC
ALL	282	50	111	2	46	6
DEL PEAK 41(XQ23) MUTATED	0	4	0	0	0	0
DEL PEAK 41(XQ23) WILD-TYPE	282	46	111	2	46	6

Figure S157. Get High-res Image Gene #95: 'del_xq23' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_xq22.3' versus 'PATHOLOGIC_STAGE'

P value = 0.00101 (Fisher's exact test), Q value = 0.078

Table S158. Gene #96: 'del_xq22.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV	STAGE IVA	STAGE IVC
ALL	282	50	111	2	46	6
DEL PEAK 42(XQ22.3) MUTATED	0	4	0	0	0	0
DEL PEAK 42(XQ22.3) WILD-TYPE	282	46	111	2	46	6

Figure S158. Get High-res Image Gene #96: 'del_xq22.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

Methods & Data

Input

Copy number data file = all_lesions.txt from GISTIC pipeline
Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/THCA-TP/19782153/transformed.cor.cli.txt
Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/THCA-TP/19775590/THCA-TP.merged_data.txt
Number of patients = 499
Number of significantly focal cnvs = 96
Number of selected clinical features = 17
Exclude genes that fewer than K tumors have mutations, K = 3

Survival analysis

For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene mutations were plotted and the statistical significance P values were estimated by logrank test (Bland and Altman 2004) using the 'survdiff' function in R

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

References

[1] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)

[2] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)

[3] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)

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