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

Sarcoma (Primary solid tumor)

21 August 2015 | analyses__2015_08_21

Maintainer Information

Citation Information

Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)

Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between copy number variation genes (focal events) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C11G0KJD

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 66 focal events and 9 clinical features across 256 patients, 183 significant findings detected with Q value < 0.25.

amp_1p32.1 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.
amp_1q21.3 cnv correlated to 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.
amp_1q24.3 cnv correlated to 'RADIATION_THERAPY'.
amp_2p11.2 cnv correlated to 'YEARS_TO_BIRTH'.
amp_3p12.1 cnv correlated to 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.
amp_4q12 cnv correlated to 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.
amp_5p15.33 cnv correlated to 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.
amp_6p21.1 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', and 'RADIATION_THERAPY'.
amp_6q25.1 cnv correlated to 'GENDER' and 'HISTOLOGICAL_TYPE'.
amp_7q31.2 cnv correlated to 'YEARS_TO_BIRTH', 'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.
amp_8p11.22 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', and 'HISTOLOGICAL_TYPE'.
amp_8q24.21 cnv correlated to 'Time to Death'.
amp_11q22.2 cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.
amp_12q15 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'GENDER', 'HISTOLOGICAL_TYPE', 'RESIDUAL_TUMOR', and 'RACE'.
amp_13q34 cnv correlated to 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', 'HISTOLOGICAL_TYPE', and 'RACE'.
amp_15q26.3 cnv correlated to 'YEARS_TO_BIRTH'.
amp_17p12 cnv correlated to 'YEARS_TO_BIRTH', 'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.
amp_17p11.2 cnv correlated to 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.
amp_17q24.3 cnv correlated to 'YEARS_TO_BIRTH', 'GENDER', 'RADIATION_THERAPY', 'HISTOLOGICAL_TYPE', and 'RESIDUAL_TUMOR'.
amp_19p13.2 cnv correlated to 'HISTOLOGICAL_TYPE'.
amp_19q12 cnv correlated to 'YEARS_TO_BIRTH', 'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.
amp_20q13.33 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'GENDER', 'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.
amp_21q21.1 cnv correlated to 'YEARS_TO_BIRTH' and 'GENDER'.
amp_xp21.2 cnv correlated to 'YEARS_TO_BIRTH', 'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.
amp_xq21.1 cnv correlated to 'YEARS_TO_BIRTH'.
del_1p36.32 cnv correlated to 'Time to Death', 'GENDER', 'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.
del_1q44 cnv correlated to 'YEARS_TO_BIRTH', 'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.
del_2p25.3 cnv correlated to 'YEARS_TO_BIRTH', 'GENDER', 'HISTOLOGICAL_TYPE', and 'RACE'.
del_2q37.3 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.
del_2q37.3 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.
del_3p21.31 cnv correlated to 'RADIATION_THERAPY' and 'HISTOLOGICAL_TYPE'.
del_3q13.31 cnv correlated to 'YEARS_TO_BIRTH' and 'RADIATION_THERAPY'.
del_4q35.1 cnv correlated to 'YEARS_TO_BIRTH', 'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.
del_5p15.33 cnv correlated to 'TUMOR_TISSUE_SITE'.
del_6p25.3 cnv correlated to 'HISTOLOGICAL_TYPE'.
del_6q14.1 cnv correlated to 'TUMOR_TISSUE_SITE' and 'RADIATION_THERAPY'.
del_8p23.3 cnv correlated to 'YEARS_TO_BIRTH' and 'RADIATION_THERAPY'.
del_9p24.3 cnv correlated to 'YEARS_TO_BIRTH'.
del_9p21.3 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', and 'HISTOLOGICAL_TYPE'.
del_9q34.3 cnv correlated to 'HISTOLOGICAL_TYPE', 'RESIDUAL_TUMOR', and 'RACE'.
del_10p15.3 cnv correlated to 'YEARS_TO_BIRTH' and 'HISTOLOGICAL_TYPE'.
del_10q23.31 cnv correlated to 'YEARS_TO_BIRTH', 'RADIATION_THERAPY', 'HISTOLOGICAL_TYPE', and 'RACE'.
del_10q26.3 cnv correlated to 'YEARS_TO_BIRTH', 'HISTOLOGICAL_TYPE', and 'RACE'.
del_11p15.5 cnv correlated to 'YEARS_TO_BIRTH' and 'RADIATION_THERAPY'.
del_11q24.2 cnv correlated to 'YEARS_TO_BIRTH', 'RADIATION_THERAPY', 'HISTOLOGICAL_TYPE', and 'RESIDUAL_TUMOR'.
del_12p13.1 cnv correlated to 'GENDER' and 'HISTOLOGICAL_TYPE'.
del_12q12 cnv correlated to 'Time to Death' and 'RACE'.
del_12q24.33 cnv correlated to 'YEARS_TO_BIRTH'.
del_13q14.2 cnv correlated to 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.
del_14q24.1 cnv correlated to 'TUMOR_TISSUE_SITE'.
del_16q11.2 cnv correlated to 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'HISTOLOGICAL_TYPE', and 'RACE'.
del_16q23.1 cnv correlated to 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', and 'HISTOLOGICAL_TYPE'.
del_17p13.1 cnv correlated to 'Time to Death', 'TUMOR_TISSUE_SITE', 'GENDER', 'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.
del_17q11.2 cnv correlated to 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.
del_17q25.3 cnv correlated to 'YEARS_TO_BIRTH'.
del_18q23 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', and 'HISTOLOGICAL_TYPE'.
del_19p13.3 cnv correlated to 'GENDER' and 'HISTOLOGICAL_TYPE'.
del_19q13.43 cnv correlated to 'Time to Death', 'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.
del_21q11.2 cnv correlated to 'HISTOLOGICAL_TYPE'.
del_21q22.3 cnv correlated to 'YEARS_TO_BIRTH' and 'HISTOLOGICAL_TYPE'.
del_22q13.32 cnv correlated to 'TUMOR_TISSUE_SITE'.
del_xp21.1 cnv correlated to 'YEARS_TO_BIRTH', 'GENDER', and 'HISTOLOGICAL_TYPE'.
del_xq21.1 cnv correlated to 'Time to Death', 'GENDER', and 'HISTOLOGICAL_TYPE'.
del_xq22.3 cnv correlated to 'Time to Death', 'TUMOR_TISSUE_SITE', 'GENDER', 'HISTOLOGICAL_TYPE', and 'RESIDUAL_TUMOR'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 66 focal events and 9 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 183 significant findings detected.


		Clinical Features	Time to Death	YEARS TO BIRTH	TUMOR TISSUE SITE	GENDER	RADIATION THERAPY	HISTOLOGICAL TYPE	RESIDUAL TUMOR	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
amp 12q15	94 (37%)	162	0.0428 (0.174)	0.0069 (0.0554)	2e-05 (0.000849)	0.000413 (0.00952)	0.466 (0.704)	1e-05 (0.00054)	0.00091 (0.0146)	0.00718 (0.0561)	1 (1.00)
amp 20q13 33	98 (38%)	158	0.031 (0.145)	0.000278 (0.0075)	0.0736 (0.243)	0.0099 (0.0684)	0.0134 (0.0831)	0.00099 (0.0151)	0.102 (0.288)	1 (1.00)	1 (1.00)
amp 1p32 1	94 (37%)	162	0.000161 (0.00503)	0.000433 (0.00952)	0.0202 (0.11)	0.196 (0.436)	0.00846 (0.0636)	0.00144 (0.0194)	0.389 (0.638)	0.135 (0.35)	0.159 (0.386)
amp 17q24 3	79 (31%)	177	0.274 (0.537)	0.0385 (0.162)	0.213 (0.45)	0.0303 (0.143)	0.022 (0.117)	0.0105 (0.0718)	0.0387 (0.162)	0.548 (0.772)	1 (1.00)
del 2q37 3	108 (42%)	148	0.0107 (0.0722)	0.00887 (0.0656)	0.025 (0.125)	1 (1.00)	0.00987 (0.0684)	0.00111 (0.0165)	0.764 (0.901)	0.503 (0.735)	0.396 (0.638)
del 2q37 3	110 (43%)	146	0.0549 (0.202)	0.00278 (0.0294)	0.00588 (0.0485)	0.613 (0.818)	0.0638 (0.223)	0.0038 (0.0353)	0.581 (0.8)	0.537 (0.762)	1 (1.00)
del 17p13 1	129 (50%)	127	0.0591 (0.213)	0.206 (0.446)	0.0542 (0.202)	0.0596 (0.213)	0.0333 (0.152)	1e-05 (0.00054)	0.54 (0.762)	0.11 (0.307)	0.683 (0.84)
del xq22 3	123 (48%)	133	0.00171 (0.0221)	0.854 (0.954)	0.00906 (0.0656)	0.0449 (0.181)	0.257 (0.518)	7e-05 (0.00231)	0.0622 (0.22)	0.654 (0.821)	0.372 (0.625)
amp 1q21 3	104 (41%)	152	0.357 (0.609)	0.0184 (0.104)	0.0454 (0.182)	0.099 (0.285)	0.0139 (0.0847)	0.00431 (0.0376)	0.363 (0.615)	0.937 (1.00)	0.651 (0.821)
amp 3p12 1	69 (27%)	187	0.203 (0.443)	1.13e-05 (0.00056)	0.00031 (0.00801)	0.396 (0.638)	0.0547 (0.202)	1e-05 (0.00054)	0.465 (0.704)	0.727 (0.871)	0.326 (0.578)
amp 4q12	78 (30%)	178	0.238 (0.489)	0.0378 (0.162)	0.023 (0.118)	0.586 (0.8)	0.00375 (0.0353)	5e-05 (0.00186)	0.523 (0.75)	0.554 (0.776)	1 (1.00)
amp 5p15 33	119 (46%)	137	0.0811 (0.261)	0.00147 (0.0194)	0.0426 (0.174)	0.168 (0.398)	0.0648 (0.224)	0.0154 (0.0925)	0.594 (0.8)	0.941 (1.00)	1 (1.00)
amp 13q34	54 (21%)	202	0.181 (0.416)	0.214 (0.45)	0.0486 (0.189)	0.0917 (0.274)	0.0246 (0.124)	0.0746 (0.245)	0.509 (0.739)	0.0367 (0.16)	0.588 (0.8)
amp 17p11 2	104 (41%)	152	0.333 (0.584)	0.0182 (0.104)	0.039 (0.162)	0.254 (0.513)	0.000838 (0.0145)	2e-05 (0.000849)	0.213 (0.45)	0.495 (0.728)	1 (1.00)
del 1p36 32	69 (27%)	187	0.0369 (0.16)	0.128 (0.342)	0.0933 (0.274)	0.000399 (0.00952)	0.00979 (0.0684)	1e-05 (0.00054)	0.113 (0.313)	0.668 (0.827)	0.328 (0.578)
del 2p25 3	94 (37%)	162	0.396 (0.638)	0.0642 (0.223)	0.286 (0.547)	0.0267 (0.132)	0.243 (0.495)	0.00142 (0.0194)	0.0876 (0.271)	0.00249 (0.0276)	0.159 (0.386)
del 10q23 31	138 (54%)	118	0.124 (0.336)	0.0204 (0.11)	0.515 (0.744)	0.211 (0.45)	0.0476 (0.187)	1e-05 (0.00054)	0.823 (0.933)	0.0168 (0.0988)	0.179 (0.415)
del 11q24 2	123 (48%)	133	0.702 (0.853)	0.0127 (0.0812)	0.18 (0.416)	0.531 (0.756)	0.0231 (0.118)	0.00897 (0.0656)	0.00431 (0.0376)	1 (1.00)	0.371 (0.624)
del 13q14 2	180 (70%)	76	0.761 (0.898)	0.00199 (0.024)	0.0109 (0.0726)	0.0998 (0.286)	0.0202 (0.11)	1e-05 (0.00054)	0.713 (0.863)	0.553 (0.776)	0.152 (0.379)
del 16q11 2	130 (51%)	126	0.849 (0.951)	0.0627 (0.22)	0.047 (0.186)	0.132 (0.345)	0.0911 (0.274)	1e-05 (0.00054)	0.274 (0.537)	0.0129 (0.0813)	1 (1.00)
del 17q11 2	81 (32%)	175	0.504 (0.735)	0.00369 (0.0353)	1e-05 (0.00054)	0.345 (0.596)	0.0098 (0.0684)	0.00042 (0.00952)	0.63 (0.821)	0.651 (0.821)	1 (1.00)
amp 6p21 1	60 (23%)	196	0.000847 (0.0145)	0.068 (0.231)	0.641 (0.821)	0.303 (0.567)	0.0311 (0.145)	0.164 (0.391)	0.303 (0.567)	0.123 (0.334)	0.336 (0.586)
amp 7q31 2	77 (30%)	179	0.0881 (0.271)	1.31e-06 (0.00054)	0.0869 (0.271)	0.891 (0.976)	0.0206 (0.11)	0.0025 (0.0276)	0.965 (1.00)	1 (1.00)	0.648 (0.821)
amp 8p11 22	81 (32%)	175	0.00751 (0.0579)	0.00121 (0.0175)	0.64 (0.821)	1 (1.00)	0.127 (0.34)	0.0578 (0.211)	0.632 (0.821)	0.0896 (0.274)	0.66 (0.826)
amp 17p12	102 (40%)	154	0.316 (0.578)	0.0167 (0.0988)	0.456 (0.698)	0.702 (0.853)	0.0616 (0.219)	0.00333 (0.033)	0.621 (0.821)	0.773 (0.908)	0.4 (0.642)
amp 19q12	93 (36%)	163	0.108 (0.304)	0.000648 (0.0133)	0.263 (0.522)	0.244 (0.495)	0.0404 (0.167)	0.0117 (0.0768)	0.457 (0.698)	0.872 (0.967)	0.654 (0.821)
amp xp21 2	97 (38%)	159	0.786 (0.913)	0.0346 (0.153)	0.282 (0.544)	0.605 (0.812)	0.0292 (0.14)	0.00716 (0.0561)	0.459 (0.699)	0.821 (0.933)	0.651 (0.821)
del 1q44	80 (31%)	176	0.195 (0.435)	0.00233 (0.0272)	0.662 (0.826)	0.787 (0.913)	0.000746 (0.0139)	5e-05 (0.00186)	0.122 (0.333)	0.228 (0.478)	1 (1.00)
del 4q35 1	94 (37%)	162	0.151 (0.378)	0.00202 (0.024)	0.234 (0.485)	0.696 (0.853)	0.00516 (0.0438)	0.00765 (0.0583)	0.198 (0.437)	0.288 (0.547)	0.161 (0.386)
del 9p21 3	114 (45%)	142	0.0538 (0.202)	0.00193 (0.024)	0.699 (0.853)	0.616 (0.82)	0.477 (0.714)	0.0268 (0.132)	0.26 (0.52)	0.505 (0.736)	1 (1.00)
del 9q34 3	61 (24%)	195	0.136 (0.352)	0.277 (0.539)	0.193 (0.435)	0.462 (0.702)	0.102 (0.288)	0.00067 (0.0133)	0.00282 (0.0294)	0.0176 (0.103)	1 (1.00)
del 10q26 3	132 (52%)	124	0.59 (0.8)	0.00294 (0.0301)	0.175 (0.41)	0.452 (0.695)	0.326 (0.578)	1e-05 (0.00054)	1 (1.00)	0.0699 (0.236)	0.194 (0.435)
del 16q23 1	134 (52%)	122	0.288 (0.547)	0.000276 (0.0075)	0.0286 (0.138)	0.132 (0.345)	0.479 (0.714)	1e-05 (0.00054)	0.0958 (0.279)	0.146 (0.369)	0.666 (0.826)
del 18q23	86 (34%)	170	0.019 (0.106)	0.00313 (0.0315)	0.732 (0.872)	0.426 (0.67)	0.1 (0.286)	0.00509 (0.0438)	0.391 (0.638)	1 (1.00)	0.665 (0.826)
del 19q13 43	106 (41%)	150	0.0589 (0.213)	0.355 (0.609)	0.291 (0.55)	0.308 (0.572)	0.00412 (0.0372)	0.00071 (0.0136)	0.138 (0.356)	0.314 (0.578)	0.39 (0.638)
del xp21 1	55 (21%)	201	0.733 (0.872)	0.0229 (0.118)	0.173 (0.407)	0.0679 (0.231)	0.735 (0.873)	0.0509 (0.196)	0.311 (0.574)	0.415 (0.658)	0.244 (0.495)
del xq21 1	114 (45%)	142	0.002 (0.024)	0.209 (0.45)	0.424 (0.668)	0.0236 (0.12)	0.776 (0.908)	0.00086 (0.0145)	0.283 (0.544)	0.302 (0.567)	0.38 (0.636)
amp 6q25 1	75 (29%)	181	0.657 (0.824)	0.0875 (0.271)	0.473 (0.709)	0.0736 (0.243)	0.167 (0.397)	0.00022 (0.00653)	0.265 (0.525)	0.932 (1.00)	0.632 (0.821)
amp 11q22 2	36 (14%)	220	0.0328 (0.151)	0.00616 (0.0501)	0.899 (0.98)	0.593 (0.8)	0.232 (0.483)	0.0916 (0.274)	0.783 (0.913)	0.162 (0.388)	0.539 (0.762)
amp 21q21 1	73 (29%)	183	0.123 (0.334)	0.00554 (0.0464)	0.493 (0.728)	0.0719 (0.241)	0.21 (0.45)	0.13 (0.345)	0.484 (0.719)	0.583 (0.8)	0.325 (0.578)
del 3p21 31	65 (25%)	191	0.342 (0.592)	0.341 (0.592)	0.0861 (0.271)	0.886 (0.973)	0.0757 (0.247)	0.00095 (0.0148)	0.434 (0.675)	0.562 (0.783)	1 (1.00)
del 3q13 31	51 (20%)	205	0.211 (0.45)	0.0123 (0.0795)	0.639 (0.821)	0.434 (0.675)	0.014 (0.0847)	0.121 (0.333)	0.093 (0.274)	0.818 (0.932)	1 (1.00)
del 6q14 1	78 (30%)	178	0.473 (0.709)	0.259 (0.519)	0.0231 (0.118)	0.892 (0.976)	0.0206 (0.11)	0.0816 (0.261)	0.872 (0.967)	0.807 (0.925)	1 (1.00)
del 8p23 3	81 (32%)	175	0.0936 (0.274)	0.0486 (0.189)	0.646 (0.821)	0.5 (0.734)	0.0511 (0.196)	0.108 (0.303)	0.202 (0.442)	0.599 (0.806)	1 (1.00)
del 10p15 3	128 (50%)	128	0.912 (0.992)	0.0285 (0.138)	0.415 (0.658)	0.132 (0.345)	0.0911 (0.274)	7e-05 (0.00231)	0.306 (0.569)	0.195 (0.435)	0.212 (0.45)
del 11p15 5	110 (43%)	146	0.393 (0.638)	0.00413 (0.0372)	0.457 (0.698)	0.613 (0.818)	0.0467 (0.186)	0.158 (0.386)	0.639 (0.821)	0.64 (0.821)	0.385 (0.638)
del 12p13 1	87 (34%)	169	0.632 (0.821)	0.156 (0.386)	0.753 (0.891)	0.0342 (0.153)	0.883 (0.973)	0.0568 (0.208)	0.818 (0.932)	0.713 (0.863)	0.663 (0.826)
del 12q12	56 (22%)	200	0.0387 (0.162)	0.14 (0.356)	0.816 (0.932)	0.652 (0.821)	0.391 (0.638)	0.413 (0.658)	0.842 (0.948)	0.0365 (0.16)	0.589 (0.8)
del 19p13 3	70 (27%)	186	0.952 (1.00)	0.561 (0.783)	0.233 (0.484)	0.0118 (0.0768)	0.638 (0.821)	0.00251 (0.0276)	0.837 (0.943)	0.724 (0.869)	0.328 (0.578)
del 21q22 3	66 (26%)	190	0.847 (0.951)	0.000661 (0.0133)	0.85 (0.951)	0.886 (0.973)	0.111 (0.307)	0.0766 (0.249)	0.528 (0.756)	0.926 (1.00)	1 (1.00)
amp 1q24 3	102 (40%)	154	0.0931 (0.274)	0.14 (0.356)	0.381 (0.636)	0.899 (0.98)	0.0301 (0.143)	0.319 (0.578)	0.592 (0.8)	0.635 (0.821)	1 (1.00)
amp 2p11 2	64 (25%)	192	0.801 (0.923)	0.00088 (0.0145)	0.947 (1.00)	0.148 (0.373)	0.512 (0.742)	0.445 (0.689)	0.719 (0.867)	0.132 (0.345)	1 (1.00)
amp 8q24 21	83 (32%)	173	0.0026 (0.028)	0.389 (0.638)	0.414 (0.658)	0.79 (0.913)	0.653 (0.821)	0.0987 (0.285)	0.194 (0.435)	0.159 (0.386)	0.334 (0.584)
amp 15q26 3	84 (33%)	172	0.583 (0.8)	0.0182 (0.104)	0.482 (0.718)	0.285 (0.547)	0.367 (0.619)	0.16 (0.386)	0.569 (0.791)	0.619 (0.821)	0.347 (0.598)
amp 19p13 2	107 (42%)	149	0.821 (0.933)	0.283 (0.544)	0.186 (0.426)	0.206 (0.446)	0.774 (0.908)	0.0678 (0.231)	0.574 (0.794)	0.731 (0.872)	0.654 (0.821)
amp xq21 1	46 (18%)	210	0.0911 (0.274)	0.0544 (0.202)	0.997 (1.00)	0.333 (0.584)	0.193 (0.435)	0.323 (0.578)	0.866 (0.965)	0.24 (0.491)	0.226 (0.473)
del 5p15 33	33 (13%)	223	0.303 (0.567)	0.958 (1.00)	0.0372 (0.16)	1 (1.00)	0.683 (0.84)	0.786 (0.913)	0.955 (1.00)	0.877 (0.968)	1 (1.00)
del 6p25 3	81 (32%)	175	0.237 (0.488)	0.837 (0.943)	0.394 (0.638)	0.789 (0.913)	1 (1.00)	0.0341 (0.153)	0.988 (1.00)	0.701 (0.853)	0.327 (0.578)
del 9p24 3	100 (39%)	156	0.202 (0.442)	0.00146 (0.0194)	0.361 (0.614)	0.522 (0.75)	0.386 (0.638)	0.826 (0.935)	0.587 (0.8)	1 (1.00)	0.653 (0.821)
del 12q24 33	69 (27%)	187	0.687 (0.843)	0.0037 (0.0353)	0.309 (0.572)	0.157 (0.386)	1 (1.00)	0.418 (0.66)	0.495 (0.728)	0.395 (0.638)	0.327 (0.578)
del 14q24 1	80 (31%)	176	0.538 (0.762)	0.958 (1.00)	0.0339 (0.153)	0.139 (0.356)	0.282 (0.544)	0.807 (0.925)	0.087 (0.271)	0.653 (0.821)	0.326 (0.578)
del 17q25 3	67 (26%)	189	0.405 (0.649)	0.0133 (0.083)	0.934 (1.00)	0.776 (0.908)	0.628 (0.821)	0.492 (0.728)	0.652 (0.821)	0.721 (0.867)	0.328 (0.578)
del 21q11 2	51 (20%)	205	0.799 (0.921)	0.177 (0.411)	0.877 (0.968)	0.531 (0.756)	0.159 (0.386)	0.0535 (0.202)	0.583 (0.8)	0.748 (0.886)	0.262 (0.522)
del 22q13 32	83 (32%)	173	0.364 (0.617)	0.188 (0.43)	0.0722 (0.241)	0.0812 (0.261)	0.449 (0.692)	0.275 (0.537)	0.872 (0.967)	1 (1.00)	1 (1.00)
del 3q29	54 (21%)	202	0.719 (0.867)	0.52 (0.749)	0.572 (0.793)	0.357 (0.609)	0.0832 (0.264)	0.267 (0.527)	0.436 (0.677)	0.322 (0.578)	1 (1.00)
del 7q36 3	71 (28%)	185	0.197 (0.437)	0.472 (0.709)	0.328 (0.578)	0.677 (0.836)	0.429 (0.671)	0.171 (0.403)	0.13 (0.345)	0.427 (0.67)	1 (1.00)

'amp_1p32.1' versus 'Time to Death'

P value = 0.000161 (logrank test), Q value = 0.005

Table S1. Gene #1: 'amp_1p32.1' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	256	94	0.5 - 188.2 (26.4)
AMP PEAK 1(1P32.1) MUTATED	94	45	0.6 - 106.5 (22.3)
AMP PEAK 1(1P32.1) WILD-TYPE	162	49	0.5 - 188.2 (32.7)

Figure S1. Get High-res Image Gene #1: 'amp_1p32.1' versus Clinical Feature #1: 'Time to Death'

'amp_1p32.1' versus 'YEARS_TO_BIRTH'

P value = 0.000433 (Wilcoxon-test), Q value = 0.0095

Table S2. Gene #1: 'amp_1p32.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
AMP PEAK 1(1P32.1) MUTATED	94	65.3 (13.0)
AMP PEAK 1(1P32.1) WILD-TYPE	161	58.4 (15.0)

Figure S2. Get High-res Image Gene #1: 'amp_1p32.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_1p32.1' versus 'TUMOR_TISSUE_SITE'

P value = 0.0202 (Fisher's exact test), Q value = 0.11

Table S3. Gene #1: 'amp_1p32.1' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	CHEST - BREAST	CHEST - CHEST WALL	CHEST - LUNG/PLEURA	CHEST - MEDIASTINUM	CHEST - OTHER (PLEASE SPECIFY	GYNECOLOGICAL - OVARY	GYNECOLOGICAL - UTERUS	HEAD AND NECK - HEAD	HEAD AND NECK - NECK	HEAD AND NECK - OTHER (PLEASE SPECIFY	LOWER ABDOMINAL/PELVIC - BLADDER	LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY	LOWER ABDOMINAL/PELVIC - PELVIC	LOWER ABDOMINAL/PELVIC - SPERMATIC CORD	LOWER EXTREMITY - FOOT/ANKLE	LOWER EXTREMITY - GROIN	LOWER EXTREMITY - LOWER LEG/CALF	LOWER EXTREMITY - OTHER (PLEASE SPECIFY	LOWER EXTREMITY - THIGH/KNEE	RETROPERITONEUM/UPPER ABDOMINAL - COLON	RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC	RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL	RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY	RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY	RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS	RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM	RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES	SUPERFICIAL TRUNK - ABDOMINAL WALL	SUPERFICIAL TRUNK - BACK	SUPERFICIAL TRUNK - BUTTOCK	SUPERFICIAL TRUNK - FLANK	UPPER EXTREMITY - SHOULDER/AXILLA	UPPER EXTREMITY - UPPER ARM/ELBOW
ALL	1	7	2	1	2	1	28	2	1	2	1	2	10	2	4	2	17	5	43	4	2	5	8	2	1	73	3	2	5	4	1	7	5
AMP PEAK 1(1P32.1) MUTATED	0	4	0	0	0	0	8	1	0	0	0	1	4	0	0	1	9	4	27	0	0	0	2	1	1	23	0	1	0	1	0	3	2
AMP PEAK 1(1P32.1) WILD-TYPE	1	3	2	1	2	1	20	1	1	2	1	1	6	2	4	1	8	1	16	4	2	5	6	1	0	50	3	1	5	3	1	4	3

Figure S3. Get High-res Image Gene #1: 'amp_1p32.1' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'amp_1p32.1' versus 'RADIATION_THERAPY'

P value = 0.00846 (Fisher's exact test), Q value = 0.064

Table S4. Gene #1: 'amp_1p32.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	180	69
AMP PEAK 1(1P32.1) MUTATED	58	35
AMP PEAK 1(1P32.1) WILD-TYPE	122	34

Figure S4. Get High-res Image Gene #1: 'amp_1p32.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_1p32.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.00144 (Fisher's exact test), Q value = 0.019

Table S5. Gene #1: 'amp_1p32.1' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	DEDIFFERENTIATED LIPOSARCOMA	DESMOID TUMOR	GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS	LEIOMYOSARCOMA (LMS)	MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)	MYXOFIBROSARCOMA	PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA	SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED	SYNOVIAL SARCOMA - BIPHASIC	SYNOVIAL SARCOMA - MONOPHASIC	UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
ALL	59	2	1	103	9	23	28	2	2	6	21
AMP PEAK 1(1P32.1) MUTATED	20	0	0	30	2	12	19	0	0	0	11
AMP PEAK 1(1P32.1) WILD-TYPE	39	2	1	73	7	11	9	2	2	6	10

Figure S5. Get High-res Image Gene #1: 'amp_1p32.1' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'amp_1q21.3' versus 'YEARS_TO_BIRTH'

P value = 0.0184 (Wilcoxon-test), Q value = 0.1

Table S6. Gene #2: 'amp_1q21.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
AMP PEAK 2(1Q21.3) MUTATED	103	63.4 (12.6)
AMP PEAK 2(1Q21.3) WILD-TYPE	152	59.2 (15.8)

Figure S6. Get High-res Image Gene #2: 'amp_1q21.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_1q21.3' versus 'TUMOR_TISSUE_SITE'

P value = 0.0454 (Fisher's exact test), Q value = 0.18

Table S7. Gene #2: 'amp_1q21.3' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	CHEST - BREAST	CHEST - CHEST WALL	CHEST - LUNG/PLEURA	CHEST - MEDIASTINUM	CHEST - OTHER (PLEASE SPECIFY	GYNECOLOGICAL - OVARY	GYNECOLOGICAL - UTERUS	HEAD AND NECK - HEAD	HEAD AND NECK - NECK	HEAD AND NECK - OTHER (PLEASE SPECIFY	LOWER ABDOMINAL/PELVIC - BLADDER	LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY	LOWER ABDOMINAL/PELVIC - PELVIC	LOWER ABDOMINAL/PELVIC - SPERMATIC CORD	LOWER EXTREMITY - FOOT/ANKLE	LOWER EXTREMITY - GROIN	LOWER EXTREMITY - LOWER LEG/CALF	LOWER EXTREMITY - OTHER (PLEASE SPECIFY	LOWER EXTREMITY - THIGH/KNEE	RETROPERITONEUM/UPPER ABDOMINAL - COLON	RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC	RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL	RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY	RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY	RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS	RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM	RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES	SUPERFICIAL TRUNK - ABDOMINAL WALL	SUPERFICIAL TRUNK - BACK	SUPERFICIAL TRUNK - BUTTOCK	SUPERFICIAL TRUNK - FLANK	UPPER EXTREMITY - SHOULDER/AXILLA	UPPER EXTREMITY - UPPER ARM/ELBOW
ALL	1	7	2	1	2	1	28	2	1	2	1	2	10	2	4	2	17	5	43	4	2	5	8	2	1	73	3	2	5	4	1	7	5
AMP PEAK 2(1Q21.3) MUTATED	0	4	1	0	0	0	20	1	0	0	0	1	2	0	1	0	11	2	22	1	1	1	2	1	1	21	0	0	2	2	0	3	3
AMP PEAK 2(1Q21.3) WILD-TYPE	1	3	1	1	2	1	8	1	1	2	1	1	8	2	3	2	6	3	21	3	1	4	6	1	0	52	3	2	3	2	1	4	2

Figure S7. Get High-res Image Gene #2: 'amp_1q21.3' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'amp_1q21.3' versus 'RADIATION_THERAPY'

P value = 0.0139 (Fisher's exact test), Q value = 0.085

Table S8. Gene #2: 'amp_1q21.3' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	180	69
AMP PEAK 2(1Q21.3) MUTATED	64	37
AMP PEAK 2(1Q21.3) WILD-TYPE	116	32

Figure S8. Get High-res Image Gene #2: 'amp_1q21.3' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_1q21.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.00431 (Fisher's exact test), Q value = 0.038

Table S9. Gene #2: 'amp_1q21.3' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	DEDIFFERENTIATED LIPOSARCOMA	DESMOID TUMOR	GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS	LEIOMYOSARCOMA (LMS)	MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)	MYXOFIBROSARCOMA	PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA	SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED	SYNOVIAL SARCOMA - BIPHASIC	SYNOVIAL SARCOMA - MONOPHASIC	UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
ALL	59	2	1	103	9	23	28	2	2	6	21
AMP PEAK 2(1Q21.3) MUTATED	15	0	0	46	3	9	18	1	0	0	12
AMP PEAK 2(1Q21.3) WILD-TYPE	44	2	1	57	6	14	10	1	2	6	9

Figure S9. Get High-res Image Gene #2: 'amp_1q21.3' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'amp_1q24.3' versus 'RADIATION_THERAPY'

P value = 0.0301 (Fisher's exact test), Q value = 0.14

Table S10. Gene #3: 'amp_1q24.3' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	180	69
AMP PEAK 3(1Q24.3) MUTATED	65	36
AMP PEAK 3(1Q24.3) WILD-TYPE	115	33

Figure S10. Get High-res Image Gene #3: 'amp_1q24.3' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_2p11.2' versus 'YEARS_TO_BIRTH'

P value = 0.00088 (Wilcoxon-test), Q value = 0.015

Table S11. Gene #4: 'amp_2p11.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
AMP PEAK 4(2P11.2) MUTATED	64	66.4 (12.5)
AMP PEAK 4(2P11.2) WILD-TYPE	191	59.1 (14.9)

Figure S11. Get High-res Image Gene #4: 'amp_2p11.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_3p12.1' versus 'YEARS_TO_BIRTH'

P value = 1.13e-05 (Wilcoxon-test), Q value = 0.00056

Table S12. Gene #5: 'amp_3p12.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
AMP PEAK 5(3P12.1) MUTATED	68	67.6 (13.7)
AMP PEAK 5(3P12.1) WILD-TYPE	187	58.5 (14.3)

Figure S12. Get High-res Image Gene #5: 'amp_3p12.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_3p12.1' versus 'TUMOR_TISSUE_SITE'

P value = 0.00031 (Fisher's exact test), Q value = 0.008

Table S13. Gene #5: 'amp_3p12.1' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	CHEST - BREAST	CHEST - CHEST WALL	CHEST - LUNG/PLEURA	CHEST - MEDIASTINUM	CHEST - OTHER (PLEASE SPECIFY	GYNECOLOGICAL - OVARY	GYNECOLOGICAL - UTERUS	HEAD AND NECK - HEAD	HEAD AND NECK - NECK	HEAD AND NECK - OTHER (PLEASE SPECIFY	LOWER ABDOMINAL/PELVIC - BLADDER	LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY	LOWER ABDOMINAL/PELVIC - PELVIC	LOWER ABDOMINAL/PELVIC - SPERMATIC CORD	LOWER EXTREMITY - FOOT/ANKLE	LOWER EXTREMITY - GROIN	LOWER EXTREMITY - LOWER LEG/CALF	LOWER EXTREMITY - OTHER (PLEASE SPECIFY	LOWER EXTREMITY - THIGH/KNEE	RETROPERITONEUM/UPPER ABDOMINAL - COLON	RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC	RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL	RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY	RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY	RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS	RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM	RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES	SUPERFICIAL TRUNK - ABDOMINAL WALL	SUPERFICIAL TRUNK - BACK	SUPERFICIAL TRUNK - BUTTOCK	SUPERFICIAL TRUNK - FLANK	UPPER EXTREMITY - SHOULDER/AXILLA	UPPER EXTREMITY - UPPER ARM/ELBOW
ALL	1	7	2	1	2	1	28	2	1	2	1	2	10	2	4	2	17	5	43	4	2	5	8	2	1	73	3	2	5	4	1	7	5
AMP PEAK 5(3P12.1) MUTATED	0	2	0	0	0	0	5	1	0	0	0	1	0	1	0	0	4	3	24	1	1	0	0	0	0	14	0	2	2	0	0	5	3
AMP PEAK 5(3P12.1) WILD-TYPE	1	5	2	1	2	1	23	1	1	2	1	1	10	1	4	2	13	2	19	3	1	5	8	2	1	59	3	0	3	4	1	2	2

Figure S13. Get High-res Image Gene #5: 'amp_3p12.1' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'amp_3p12.1' versus 'RADIATION_THERAPY'

P value = 0.0547 (Fisher's exact test), Q value = 0.2

Table S14. Gene #5: 'amp_3p12.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	180	69
AMP PEAK 5(3P12.1) MUTATED	42	25
AMP PEAK 5(3P12.1) WILD-TYPE	138	44

Figure S14. Get High-res Image Gene #5: 'amp_3p12.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_3p12.1' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00054

Table S15. Gene #5: 'amp_3p12.1' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	DEDIFFERENTIATED LIPOSARCOMA	DESMOID TUMOR	GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS	LEIOMYOSARCOMA (LMS)	MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)	MYXOFIBROSARCOMA	PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA	SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED	SYNOVIAL SARCOMA - BIPHASIC	SYNOVIAL SARCOMA - MONOPHASIC	UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
ALL	59	2	1	103	9	23	28	2	2	6	21
AMP PEAK 5(3P12.1) MUTATED	10	0	0	21	0	9	18	0	0	0	11
AMP PEAK 5(3P12.1) WILD-TYPE	49	2	1	82	9	14	10	2	2	6	10

Figure S15. Get High-res Image Gene #5: 'amp_3p12.1' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'amp_4q12' versus 'YEARS_TO_BIRTH'

P value = 0.0378 (Wilcoxon-test), Q value = 0.16

Table S16. Gene #6: 'amp_4q12' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
AMP PEAK 6(4Q12) MUTATED	77	64.1 (12.3)
AMP PEAK 6(4Q12) WILD-TYPE	178	59.6 (15.4)

Figure S16. Get High-res Image Gene #6: 'amp_4q12' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_4q12' versus 'TUMOR_TISSUE_SITE'

P value = 0.023 (Fisher's exact test), Q value = 0.12

Table S17. Gene #6: 'amp_4q12' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	CHEST - BREAST	CHEST - CHEST WALL	CHEST - LUNG/PLEURA	CHEST - MEDIASTINUM	CHEST - OTHER (PLEASE SPECIFY	GYNECOLOGICAL - OVARY	GYNECOLOGICAL - UTERUS	HEAD AND NECK - HEAD	HEAD AND NECK - NECK	HEAD AND NECK - OTHER (PLEASE SPECIFY	LOWER ABDOMINAL/PELVIC - BLADDER	LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY	LOWER ABDOMINAL/PELVIC - PELVIC	LOWER ABDOMINAL/PELVIC - SPERMATIC CORD	LOWER EXTREMITY - FOOT/ANKLE	LOWER EXTREMITY - GROIN	LOWER EXTREMITY - LOWER LEG/CALF	LOWER EXTREMITY - OTHER (PLEASE SPECIFY	LOWER EXTREMITY - THIGH/KNEE	RETROPERITONEUM/UPPER ABDOMINAL - COLON	RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC	RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL	RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY	RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY	RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS	RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM	RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES	SUPERFICIAL TRUNK - ABDOMINAL WALL	SUPERFICIAL TRUNK - BACK	SUPERFICIAL TRUNK - BUTTOCK	SUPERFICIAL TRUNK - FLANK	UPPER EXTREMITY - SHOULDER/AXILLA	UPPER EXTREMITY - UPPER ARM/ELBOW
ALL	1	7	2	1	2	1	28	2	1	2	1	2	10	2	4	2	17	5	43	4	2	5	8	2	1	73	3	2	5	4	1	7	5
AMP PEAK 6(4Q12) MUTATED	0	4	0	0	0	0	7	2	0	0	0	1	2	0	0	1	6	4	20	1	1	1	1	0	0	16	0	2	0	2	0	5	2
AMP PEAK 6(4Q12) WILD-TYPE	1	3	2	1	2	1	21	0	1	2	1	1	8	2	4	1	11	1	23	3	1	4	7	2	1	57	3	0	5	2	1	2	3

Figure S17. Get High-res Image Gene #6: 'amp_4q12' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'amp_4q12' versus 'RADIATION_THERAPY'

P value = 0.00375 (Fisher's exact test), Q value = 0.035

Table S18. Gene #6: 'amp_4q12' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	180	69
AMP PEAK 6(4Q12) MUTATED	46	31
AMP PEAK 6(4Q12) WILD-TYPE	134	38

Figure S18. Get High-res Image Gene #6: 'amp_4q12' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_4q12' versus 'HISTOLOGICAL_TYPE'

P value = 5e-05 (Fisher's exact test), Q value = 0.0019

Table S19. Gene #6: 'amp_4q12' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	DEDIFFERENTIATED LIPOSARCOMA	DESMOID TUMOR	GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS	LEIOMYOSARCOMA (LMS)	MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)	MYXOFIBROSARCOMA	PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA	SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED	SYNOVIAL SARCOMA - BIPHASIC	SYNOVIAL SARCOMA - MONOPHASIC	UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
ALL	59	2	1	103	9	23	28	2	2	6	21
AMP PEAK 6(4Q12) MUTATED	11	0	0	23	3	12	15	1	0	0	13
AMP PEAK 6(4Q12) WILD-TYPE	48	2	1	80	6	11	13	1	2	6	8

Figure S19. Get High-res Image Gene #6: 'amp_4q12' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'amp_5p15.33' versus 'YEARS_TO_BIRTH'

P value = 0.00147 (Wilcoxon-test), Q value = 0.019

Table S20. Gene #7: 'amp_5p15.33' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
AMP PEAK 7(5P15.33) MUTATED	118	64.1 (13.3)
AMP PEAK 7(5P15.33) WILD-TYPE	137	58.2 (15.3)

Figure S20. Get High-res Image Gene #7: 'amp_5p15.33' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_5p15.33' versus 'TUMOR_TISSUE_SITE'

P value = 0.0426 (Fisher's exact test), Q value = 0.17

Table S21. Gene #7: 'amp_5p15.33' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	CHEST - BREAST	CHEST - CHEST WALL	CHEST - LUNG/PLEURA	CHEST - MEDIASTINUM	CHEST - OTHER (PLEASE SPECIFY	GYNECOLOGICAL - OVARY	GYNECOLOGICAL - UTERUS	HEAD AND NECK - HEAD	HEAD AND NECK - NECK	HEAD AND NECK - OTHER (PLEASE SPECIFY	LOWER ABDOMINAL/PELVIC - BLADDER	LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY	LOWER ABDOMINAL/PELVIC - PELVIC	LOWER ABDOMINAL/PELVIC - SPERMATIC CORD	LOWER EXTREMITY - FOOT/ANKLE	LOWER EXTREMITY - GROIN	LOWER EXTREMITY - LOWER LEG/CALF	LOWER EXTREMITY - OTHER (PLEASE SPECIFY	LOWER EXTREMITY - THIGH/KNEE	RETROPERITONEUM/UPPER ABDOMINAL - COLON	RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC	RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL	RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY	RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY	RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS	RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM	RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES	SUPERFICIAL TRUNK - ABDOMINAL WALL	SUPERFICIAL TRUNK - BACK	SUPERFICIAL TRUNK - BUTTOCK	SUPERFICIAL TRUNK - FLANK	UPPER EXTREMITY - SHOULDER/AXILLA	UPPER EXTREMITY - UPPER ARM/ELBOW
ALL	1	7	2	1	2	1	28	2	1	2	1	2	10	2	4	2	17	5	43	4	2	5	8	2	1	73	3	2	5	4	1	7	5
AMP PEAK 7(5P15.33) MUTATED	0	3	0	0	1	0	10	2	0	1	0	2	3	1	0	0	8	3	22	0	1	2	2	2	1	38	0	2	2	2	0	7	3
AMP PEAK 7(5P15.33) WILD-TYPE	1	4	2	1	1	1	18	0	1	1	1	0	7	1	4	2	9	2	21	4	1	3	6	0	0	35	3	0	3	2	1	0	2

Figure S21. Get High-res Image Gene #7: 'amp_5p15.33' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'amp_5p15.33' versus 'RADIATION_THERAPY'

P value = 0.0648 (Fisher's exact test), Q value = 0.22

Table S22. Gene #7: 'amp_5p15.33' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	180	69
AMP PEAK 7(5P15.33) MUTATED	77	39
AMP PEAK 7(5P15.33) WILD-TYPE	103	30

Figure S22. Get High-res Image Gene #7: 'amp_5p15.33' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_5p15.33' versus 'HISTOLOGICAL_TYPE'

P value = 0.0154 (Fisher's exact test), Q value = 0.092

Table S23. Gene #7: 'amp_5p15.33' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	DEDIFFERENTIATED LIPOSARCOMA	DESMOID TUMOR	GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS	LEIOMYOSARCOMA (LMS)	MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)	MYXOFIBROSARCOMA	PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA	SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED	SYNOVIAL SARCOMA - BIPHASIC	SYNOVIAL SARCOMA - MONOPHASIC	UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
ALL	59	2	1	103	9	23	28	2	2	6	21
AMP PEAK 7(5P15.33) MUTATED	28	0	0	42	6	11	20	1	0	0	11
AMP PEAK 7(5P15.33) WILD-TYPE	31	2	1	61	3	12	8	1	2	6	10

Figure S23. Get High-res Image Gene #7: 'amp_5p15.33' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'amp_6p21.1' versus 'Time to Death'

P value = 0.000847 (logrank test), Q value = 0.015

Table S24. Gene #8: 'amp_6p21.1' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	256	94	0.5 - 188.2 (26.4)
AMP PEAK 8(6P21.1) MUTATED	60	32	0.6 - 143.4 (22.7)
AMP PEAK 8(6P21.1) WILD-TYPE	196	62	0.5 - 188.2 (27.4)

Figure S24. Get High-res Image Gene #8: 'amp_6p21.1' versus Clinical Feature #1: 'Time to Death'

'amp_6p21.1' versus 'YEARS_TO_BIRTH'

P value = 0.068 (Wilcoxon-test), Q value = 0.23

Table S25. Gene #8: 'amp_6p21.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
AMP PEAK 8(6P21.1) MUTATED	59	63.8 (13.2)
AMP PEAK 8(6P21.1) WILD-TYPE	196	60.1 (15.0)

Figure S25. Get High-res Image Gene #8: 'amp_6p21.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_6p21.1' versus 'RADIATION_THERAPY'

P value = 0.0311 (Fisher's exact test), Q value = 0.14

Table S26. Gene #8: 'amp_6p21.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	180	69
AMP PEAK 8(6P21.1) MUTATED	36	23
AMP PEAK 8(6P21.1) WILD-TYPE	144	46

Figure S26. Get High-res Image Gene #8: 'amp_6p21.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_6q25.1' versus 'GENDER'

P value = 0.0736 (Fisher's exact test), Q value = 0.24

Table S27. Gene #9: 'amp_6q25.1' versus Clinical Feature #4: 'GENDER'

nPatients	FEMALE	MALE
ALL	139	117
AMP PEAK 9(6Q25.1) MUTATED	34	41
AMP PEAK 9(6Q25.1) WILD-TYPE	105	76

Figure S27. Get High-res Image Gene #9: 'amp_6q25.1' versus Clinical Feature #4: 'GENDER'

'amp_6q25.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.00022 (Fisher's exact test), Q value = 0.0065

Table S28. Gene #9: 'amp_6q25.1' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	DEDIFFERENTIATED LIPOSARCOMA	DESMOID TUMOR	GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS	LEIOMYOSARCOMA (LMS)	MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)	MYXOFIBROSARCOMA	PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA	SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED	SYNOVIAL SARCOMA - BIPHASIC	SYNOVIAL SARCOMA - MONOPHASIC	UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
ALL	59	2	1	103	9	23	28	2	2	6	21
AMP PEAK 9(6Q25.1) MUTATED	24	0	0	17	2	12	15	0	0	0	5
AMP PEAK 9(6Q25.1) WILD-TYPE	35	2	1	86	7	11	13	2	2	6	16

Figure S28. Get High-res Image Gene #9: 'amp_6q25.1' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'amp_7q31.2' versus 'YEARS_TO_BIRTH'

P value = 1.31e-06 (Wilcoxon-test), Q value = 0.00054

Table S29. Gene #10: 'amp_7q31.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
AMP PEAK 10(7Q31.2) MUTATED	77	67.3 (11.9)
AMP PEAK 10(7Q31.2) WILD-TYPE	178	58.2 (14.9)

Figure S29. Get High-res Image Gene #10: 'amp_7q31.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_7q31.2' versus 'RADIATION_THERAPY'

P value = 0.0206 (Fisher's exact test), Q value = 0.11

Table S30. Gene #10: 'amp_7q31.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	180	69
AMP PEAK 10(7Q31.2) MUTATED	47	29
AMP PEAK 10(7Q31.2) WILD-TYPE	133	40

Figure S30. Get High-res Image Gene #10: 'amp_7q31.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_7q31.2' versus 'HISTOLOGICAL_TYPE'

P value = 0.0025 (Fisher's exact test), Q value = 0.028

Table S31. Gene #10: 'amp_7q31.2' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	DEDIFFERENTIATED LIPOSARCOMA	DESMOID TUMOR	GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS	LEIOMYOSARCOMA (LMS)	MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)	MYXOFIBROSARCOMA	PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA	SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED	SYNOVIAL SARCOMA - BIPHASIC	SYNOVIAL SARCOMA - MONOPHASIC	UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
ALL	59	2	1	103	9	23	28	2	2	6	21
AMP PEAK 10(7Q31.2) MUTATED	18	0	0	20	3	10	14	0	0	0	12
AMP PEAK 10(7Q31.2) WILD-TYPE	41	2	1	83	6	13	14	2	2	6	9

Figure S31. Get High-res Image Gene #10: 'amp_7q31.2' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'amp_8p11.22' versus 'Time to Death'

P value = 0.00751 (logrank test), Q value = 0.058

Table S32. Gene #11: 'amp_8p11.22' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	256	94	0.5 - 188.2 (26.4)
AMP PEAK 11(8P11.22) MUTATED	81	38	0.6 - 112.0 (22.6)
AMP PEAK 11(8P11.22) WILD-TYPE	175	56	0.5 - 188.2 (29.5)

Figure S32. Get High-res Image Gene #11: 'amp_8p11.22' versus Clinical Feature #1: 'Time to Death'

'amp_8p11.22' versus 'YEARS_TO_BIRTH'

P value = 0.00121 (Wilcoxon-test), Q value = 0.017

Table S33. Gene #11: 'amp_8p11.22' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
AMP PEAK 11(8P11.22) MUTATED	80	65.6 (12.2)
AMP PEAK 11(8P11.22) WILD-TYPE	175	58.8 (15.3)

Figure S33. Get High-res Image Gene #11: 'amp_8p11.22' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_8p11.22' versus 'HISTOLOGICAL_TYPE'

P value = 0.0578 (Fisher's exact test), Q value = 0.21

Table S34. Gene #11: 'amp_8p11.22' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	DEDIFFERENTIATED LIPOSARCOMA	DESMOID TUMOR	GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS	LEIOMYOSARCOMA (LMS)	MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)	MYXOFIBROSARCOMA	PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA	SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED	SYNOVIAL SARCOMA - BIPHASIC	SYNOVIAL SARCOMA - MONOPHASIC	UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
ALL	59	2	1	103	9	23	28	2	2	6	21
AMP PEAK 11(8P11.22) MUTATED	14	0	0	32	1	12	13	0	0	0	9
AMP PEAK 11(8P11.22) WILD-TYPE	45	2	1	71	8	11	15	2	2	6	12

Figure S34. Get High-res Image Gene #11: 'amp_8p11.22' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'amp_8q24.21' versus 'Time to Death'

P value = 0.0026 (logrank test), Q value = 0.028

Table S35. Gene #12: 'amp_8q24.21' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	256	94	0.5 - 188.2 (26.4)
AMP PEAK 12(8Q24.21) MUTATED	83	37	0.6 - 88.3 (19.5)
AMP PEAK 12(8Q24.21) WILD-TYPE	173	57	0.5 - 188.2 (32.1)

Figure S35. Get High-res Image Gene #12: 'amp_8q24.21' versus Clinical Feature #1: 'Time to Death'

'amp_11q22.2' versus 'Time to Death'

P value = 0.0328 (logrank test), Q value = 0.15

Table S36. Gene #13: 'amp_11q22.2' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	256	94	0.5 - 188.2 (26.4)
AMP PEAK 13(11Q22.2) MUTATED	36	18	0.7 - 106.5 (20.8)
AMP PEAK 13(11Q22.2) WILD-TYPE	220	76	0.5 - 188.2 (28.1)

Figure S36. Get High-res Image Gene #13: 'amp_11q22.2' versus Clinical Feature #1: 'Time to Death'

'amp_11q22.2' versus 'YEARS_TO_BIRTH'

P value = 0.00616 (Wilcoxon-test), Q value = 0.05

Table S37. Gene #13: 'amp_11q22.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
AMP PEAK 13(11Q22.2) MUTATED	36	66.8 (14.3)
AMP PEAK 13(11Q22.2) WILD-TYPE	219	60.0 (14.6)

Figure S37. Get High-res Image Gene #13: 'amp_11q22.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_12q15' versus 'Time to Death'

P value = 0.0428 (logrank test), Q value = 0.17

Table S38. Gene #14: 'amp_12q15' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	256	94	0.5 - 188.2 (26.4)
AMP PEAK 14(12Q15) MUTATED	94	41	0.6 - 124.7 (28.4)
AMP PEAK 14(12Q15) WILD-TYPE	162	53	0.5 - 188.2 (25.9)

Figure S38. Get High-res Image Gene #14: 'amp_12q15' versus Clinical Feature #1: 'Time to Death'

'amp_12q15' versus 'YEARS_TO_BIRTH'

P value = 0.0069 (Wilcoxon-test), Q value = 0.055

Table S39. Gene #14: 'amp_12q15' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
AMP PEAK 14(12Q15) MUTATED	94	64.1 (13.7)
AMP PEAK 14(12Q15) WILD-TYPE	161	59.1 (15.0)

Figure S39. Get High-res Image Gene #14: 'amp_12q15' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_12q15' versus 'TUMOR_TISSUE_SITE'

P value = 2e-05 (Fisher's exact test), Q value = 0.00085

Table S40. Gene #14: 'amp_12q15' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	CHEST - BREAST	CHEST - CHEST WALL	CHEST - LUNG/PLEURA	CHEST - MEDIASTINUM	CHEST - OTHER (PLEASE SPECIFY	GYNECOLOGICAL - OVARY	GYNECOLOGICAL - UTERUS	HEAD AND NECK - HEAD	HEAD AND NECK - NECK	HEAD AND NECK - OTHER (PLEASE SPECIFY	LOWER ABDOMINAL/PELVIC - BLADDER	LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY	LOWER ABDOMINAL/PELVIC - PELVIC	LOWER ABDOMINAL/PELVIC - SPERMATIC CORD	LOWER EXTREMITY - FOOT/ANKLE	LOWER EXTREMITY - GROIN	LOWER EXTREMITY - LOWER LEG/CALF	LOWER EXTREMITY - OTHER (PLEASE SPECIFY	LOWER EXTREMITY - THIGH/KNEE	RETROPERITONEUM/UPPER ABDOMINAL - COLON	RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC	RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL	RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY	RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY	RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS	RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM	RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES	SUPERFICIAL TRUNK - ABDOMINAL WALL	SUPERFICIAL TRUNK - BACK	SUPERFICIAL TRUNK - BUTTOCK	SUPERFICIAL TRUNK - FLANK	UPPER EXTREMITY - SHOULDER/AXILLA	UPPER EXTREMITY - UPPER ARM/ELBOW
ALL	1	7	2	1	2	1	28	2	1	2	1	2	10	2	4	2	17	5	43	4	2	5	8	2	1	73	3	2	5	4	1	7	5
AMP PEAK 14(12Q15) MUTATED	0	4	0	0	1	0	3	0	0	0	0	0	3	1	0	2	4	2	9	0	1	3	2	1	0	47	0	1	3	0	0	3	3
AMP PEAK 14(12Q15) WILD-TYPE	1	3	2	1	1	1	25	2	1	2	1	2	7	1	4	0	13	3	34	4	1	2	6	1	1	26	3	1	2	4	1	4	2

Figure S40. Get High-res Image Gene #14: 'amp_12q15' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'amp_12q15' versus 'GENDER'

P value = 0.000413 (Fisher's exact test), Q value = 0.0095

Table S41. Gene #14: 'amp_12q15' versus Clinical Feature #4: 'GENDER'

nPatients	FEMALE	MALE
ALL	139	117
AMP PEAK 14(12Q15) MUTATED	37	57
AMP PEAK 14(12Q15) WILD-TYPE	102	60

Figure S41. Get High-res Image Gene #14: 'amp_12q15' versus Clinical Feature #4: 'GENDER'

'amp_12q15' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00054

Table S42. Gene #14: 'amp_12q15' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	DEDIFFERENTIATED LIPOSARCOMA	DESMOID TUMOR	GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS	LEIOMYOSARCOMA (LMS)	MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)	MYXOFIBROSARCOMA	PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA	SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED	SYNOVIAL SARCOMA - BIPHASIC	SYNOVIAL SARCOMA - MONOPHASIC	UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
ALL	59	2	1	103	9	23	28	2	2	6	21
AMP PEAK 14(12Q15) MUTATED	52	0	0	10	5	9	9	1	0	0	8
AMP PEAK 14(12Q15) WILD-TYPE	7	2	1	93	4	14	19	1	2	6	13

Figure S42. Get High-res Image Gene #14: 'amp_12q15' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'amp_12q15' versus 'RESIDUAL_TUMOR'

P value = 0.00091 (Fisher's exact test), Q value = 0.015

Table S43. Gene #14: 'amp_12q15' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	152	68	9	26
AMP PEAK 14(12Q15) MUTATED	42	38	4	9
AMP PEAK 14(12Q15) WILD-TYPE	110	30	5	17

Figure S43. Get High-res Image Gene #14: 'amp_12q15' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'amp_12q15' versus 'RACE'

P value = 0.00718 (Fisher's exact test), Q value = 0.056

Table S44. Gene #14: 'amp_12q15' versus Clinical Feature #8: 'RACE'

nPatients	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	6	18	223
AMP PEAK 14(12Q15) MUTATED	3	1	86
AMP PEAK 14(12Q15) WILD-TYPE	3	17	137

Figure S44. Get High-res Image Gene #14: 'amp_12q15' versus Clinical Feature #8: 'RACE'

'amp_13q34' versus 'TUMOR_TISSUE_SITE'

P value = 0.0486 (Fisher's exact test), Q value = 0.19

Table S45. Gene #15: 'amp_13q34' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	CHEST - BREAST	CHEST - CHEST WALL	CHEST - LUNG/PLEURA	CHEST - MEDIASTINUM	CHEST - OTHER (PLEASE SPECIFY	GYNECOLOGICAL - OVARY	GYNECOLOGICAL - UTERUS	HEAD AND NECK - HEAD	HEAD AND NECK - NECK	HEAD AND NECK - OTHER (PLEASE SPECIFY	LOWER ABDOMINAL/PELVIC - BLADDER	LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY	LOWER ABDOMINAL/PELVIC - PELVIC	LOWER ABDOMINAL/PELVIC - SPERMATIC CORD	LOWER EXTREMITY - FOOT/ANKLE	LOWER EXTREMITY - GROIN	LOWER EXTREMITY - LOWER LEG/CALF	LOWER EXTREMITY - OTHER (PLEASE SPECIFY	LOWER EXTREMITY - THIGH/KNEE	RETROPERITONEUM/UPPER ABDOMINAL - COLON	RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC	RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL	RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY	RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY	RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS	RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM	RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES	SUPERFICIAL TRUNK - ABDOMINAL WALL	SUPERFICIAL TRUNK - BACK	SUPERFICIAL TRUNK - BUTTOCK	SUPERFICIAL TRUNK - FLANK	UPPER EXTREMITY - SHOULDER/AXILLA	UPPER EXTREMITY - UPPER ARM/ELBOW
ALL	1	7	2	1	2	1	28	2	1	2	1	2	10	2	4	2	17	5	43	4	2	5	8	2	1	73	3	2	5	4	1	7	5
AMP PEAK 15(13Q34) MUTATED	0	3	0	0	0	0	8	0	0	0	0	2	3	0	0	1	4	2	16	0	0	0	0	0	0	7	1	0	0	2	0	3	2
AMP PEAK 15(13Q34) WILD-TYPE	1	4	2	1	2	1	20	2	1	2	1	0	7	2	4	1	13	3	27	4	2	5	8	2	1	66	2	2	5	2	1	4	3

Figure S45. Get High-res Image Gene #15: 'amp_13q34' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'amp_13q34' versus 'RADIATION_THERAPY'

P value = 0.0246 (Fisher's exact test), Q value = 0.12

Table S46. Gene #15: 'amp_13q34' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	180	69
AMP PEAK 15(13Q34) MUTATED	32	22
AMP PEAK 15(13Q34) WILD-TYPE	148	47

Figure S46. Get High-res Image Gene #15: 'amp_13q34' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_13q34' versus 'HISTOLOGICAL_TYPE'

P value = 0.0746 (Fisher's exact test), Q value = 0.24

Table S47. Gene #15: 'amp_13q34' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	DEDIFFERENTIATED LIPOSARCOMA	DESMOID TUMOR	GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS	LEIOMYOSARCOMA (LMS)	MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)	MYXOFIBROSARCOMA	PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA	SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED	SYNOVIAL SARCOMA - BIPHASIC	SYNOVIAL SARCOMA - MONOPHASIC	UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
ALL	59	2	1	103	9	23	28	2	2	6	21
AMP PEAK 15(13Q34) MUTATED	5	0	0	23	2	8	9	1	0	0	6
AMP PEAK 15(13Q34) WILD-TYPE	54	2	1	80	7	15	19	1	2	6	15

Figure S47. Get High-res Image Gene #15: 'amp_13q34' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'amp_13q34' versus 'RACE'

P value = 0.0367 (Fisher's exact test), Q value = 0.16

Table S48. Gene #15: 'amp_13q34' versus Clinical Feature #8: 'RACE'

nPatients	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	6	18	223
AMP PEAK 15(13Q34) MUTATED	0	8	45
AMP PEAK 15(13Q34) WILD-TYPE	6	10	178

Figure S48. Get High-res Image Gene #15: 'amp_13q34' versus Clinical Feature #8: 'RACE'

'amp_15q26.3' versus 'YEARS_TO_BIRTH'

P value = 0.0182 (Wilcoxon-test), Q value = 0.1

Table S49. Gene #16: 'amp_15q26.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
AMP PEAK 16(15Q26.3) MUTATED	83	63.7 (14.5)
AMP PEAK 16(15Q26.3) WILD-TYPE	172	59.6 (14.6)

Figure S49. Get High-res Image Gene #16: 'amp_15q26.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_17p12' versus 'YEARS_TO_BIRTH'

P value = 0.0167 (Wilcoxon-test), Q value = 0.099

Table S50. Gene #17: 'amp_17p12' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
AMP PEAK 17(17P12) MUTATED	101	63.8 (13.7)
AMP PEAK 17(17P12) WILD-TYPE	154	59.1 (15.0)

Figure S50. Get High-res Image Gene #17: 'amp_17p12' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_17p12' versus 'RADIATION_THERAPY'

P value = 0.0616 (Fisher's exact test), Q value = 0.22

Table S51. Gene #17: 'amp_17p12' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	180	69
AMP PEAK 17(17P12) MUTATED	65	34
AMP PEAK 17(17P12) WILD-TYPE	115	35

Figure S51. Get High-res Image Gene #17: 'amp_17p12' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_17p12' versus 'HISTOLOGICAL_TYPE'

P value = 0.00333 (Fisher's exact test), Q value = 0.033

Table S52. Gene #17: 'amp_17p12' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	DEDIFFERENTIATED LIPOSARCOMA	DESMOID TUMOR	GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS	LEIOMYOSARCOMA (LMS)	MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)	MYXOFIBROSARCOMA	PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA	SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED	SYNOVIAL SARCOMA - BIPHASIC	SYNOVIAL SARCOMA - MONOPHASIC	UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
ALL	59	2	1	103	9	23	28	2	2	6	21
AMP PEAK 17(17P12) MUTATED	14	0	0	48	3	11	12	0	0	0	14
AMP PEAK 17(17P12) WILD-TYPE	45	2	1	55	6	12	16	2	2	6	7

Figure S52. Get High-res Image Gene #17: 'amp_17p12' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'amp_17p11.2' versus 'YEARS_TO_BIRTH'

P value = 0.0182 (Wilcoxon-test), Q value = 0.1

Table S53. Gene #18: 'amp_17p11.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
AMP PEAK 18(17P11.2) MUTATED	103	63.6 (13.8)
AMP PEAK 18(17P11.2) WILD-TYPE	152	59.1 (15.0)

Figure S53. Get High-res Image Gene #18: 'amp_17p11.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_17p11.2' versus 'TUMOR_TISSUE_SITE'

P value = 0.039 (Fisher's exact test), Q value = 0.16

Table S54. Gene #18: 'amp_17p11.2' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	CHEST - BREAST	CHEST - CHEST WALL	CHEST - LUNG/PLEURA	CHEST - MEDIASTINUM	CHEST - OTHER (PLEASE SPECIFY	GYNECOLOGICAL - OVARY	GYNECOLOGICAL - UTERUS	HEAD AND NECK - HEAD	HEAD AND NECK - NECK	HEAD AND NECK - OTHER (PLEASE SPECIFY	LOWER ABDOMINAL/PELVIC - BLADDER	LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY	LOWER ABDOMINAL/PELVIC - PELVIC	LOWER ABDOMINAL/PELVIC - SPERMATIC CORD	LOWER EXTREMITY - FOOT/ANKLE	LOWER EXTREMITY - GROIN	LOWER EXTREMITY - LOWER LEG/CALF	LOWER EXTREMITY - OTHER (PLEASE SPECIFY	LOWER EXTREMITY - THIGH/KNEE	RETROPERITONEUM/UPPER ABDOMINAL - COLON	RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC	RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL	RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY	RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY	RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS	RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM	RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES	SUPERFICIAL TRUNK - ABDOMINAL WALL	SUPERFICIAL TRUNK - BACK	SUPERFICIAL TRUNK - BUTTOCK	SUPERFICIAL TRUNK - FLANK	UPPER EXTREMITY - SHOULDER/AXILLA	UPPER EXTREMITY - UPPER ARM/ELBOW
ALL	1	7	2	1	2	1	28	2	1	2	1	2	10	2	4	2	17	5	43	4	2	5	8	2	1	73	3	2	5	4	1	7	5
AMP PEAK 18(17P11.2) MUTATED	0	4	0	1	2	1	12	1	0	0	0	0	2	0	0	1	13	4	22	1	1	1	2	1	0	22	2	0	2	2	0	4	2
AMP PEAK 18(17P11.2) WILD-TYPE	1	3	2	0	0	0	16	1	1	2	1	2	8	2	4	1	4	1	21	3	1	4	6	1	1	51	1	2	3	2	1	3	3

Figure S54. Get High-res Image Gene #18: 'amp_17p11.2' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'amp_17p11.2' versus 'RADIATION_THERAPY'

P value = 0.000838 (Fisher's exact test), Q value = 0.015

Table S55. Gene #18: 'amp_17p11.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	180	69
AMP PEAK 18(17P11.2) MUTATED	61	40
AMP PEAK 18(17P11.2) WILD-TYPE	119	29

Figure S55. Get High-res Image Gene #18: 'amp_17p11.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_17p11.2' versus 'HISTOLOGICAL_TYPE'

P value = 2e-05 (Fisher's exact test), Q value = 0.00085

Table S56. Gene #18: 'amp_17p11.2' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	DEDIFFERENTIATED LIPOSARCOMA	DESMOID TUMOR	GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS	LEIOMYOSARCOMA (LMS)	MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)	MYXOFIBROSARCOMA	PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA	SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED	SYNOVIAL SARCOMA - BIPHASIC	SYNOVIAL SARCOMA - MONOPHASIC	UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
ALL	59	2	1	103	9	23	28	2	2	6	21
AMP PEAK 18(17P11.2) MUTATED	11	0	0	46	3	13	16	0	0	0	15
AMP PEAK 18(17P11.2) WILD-TYPE	48	2	1	57	6	10	12	2	2	6	6

Figure S56. Get High-res Image Gene #18: 'amp_17p11.2' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'amp_17q24.3' versus 'YEARS_TO_BIRTH'

P value = 0.0385 (Wilcoxon-test), Q value = 0.16

Table S57. Gene #19: 'amp_17q24.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
AMP PEAK 19(17Q24.3) MUTATED	78	63.8 (14.1)
AMP PEAK 19(17Q24.3) WILD-TYPE	177	59.7 (14.8)

Figure S57. Get High-res Image Gene #19: 'amp_17q24.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_17q24.3' versus 'GENDER'

P value = 0.0303 (Fisher's exact test), Q value = 0.14

Table S58. Gene #19: 'amp_17q24.3' versus Clinical Feature #4: 'GENDER'

nPatients	FEMALE	MALE
ALL	139	117
AMP PEAK 19(17Q24.3) MUTATED	51	28
AMP PEAK 19(17Q24.3) WILD-TYPE	88	89

Figure S58. Get High-res Image Gene #19: 'amp_17q24.3' versus Clinical Feature #4: 'GENDER'

'amp_17q24.3' versus 'RADIATION_THERAPY'

P value = 0.022 (Fisher's exact test), Q value = 0.12

Table S59. Gene #19: 'amp_17q24.3' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	180	69
AMP PEAK 19(17Q24.3) MUTATED	48	29
AMP PEAK 19(17Q24.3) WILD-TYPE	132	40

Figure S59. Get High-res Image Gene #19: 'amp_17q24.3' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_17q24.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.0105 (Fisher's exact test), Q value = 0.072

Table S60. Gene #19: 'amp_17q24.3' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	DEDIFFERENTIATED LIPOSARCOMA	DESMOID TUMOR	GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS	LEIOMYOSARCOMA (LMS)	MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)	MYXOFIBROSARCOMA	PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA	SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED	SYNOVIAL SARCOMA - BIPHASIC	SYNOVIAL SARCOMA - MONOPHASIC	UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
ALL	59	2	1	103	9	23	28	2	2	6	21
AMP PEAK 19(17Q24.3) MUTATED	13	0	0	27	6	12	12	0	0	0	9
AMP PEAK 19(17Q24.3) WILD-TYPE	46	2	1	76	3	11	16	2	2	6	12

Figure S60. Get High-res Image Gene #19: 'amp_17q24.3' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'amp_17q24.3' versus 'RESIDUAL_TUMOR'

P value = 0.0387 (Fisher's exact test), Q value = 0.16

Table S61. Gene #19: 'amp_17q24.3' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	152	68	9	26
AMP PEAK 19(17Q24.3) MUTATED	42	18	5	13
AMP PEAK 19(17Q24.3) WILD-TYPE	110	50	4	13

Figure S61. Get High-res Image Gene #19: 'amp_17q24.3' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'amp_19p13.2' versus 'HISTOLOGICAL_TYPE'

P value = 0.0678 (Fisher's exact test), Q value = 0.23

Table S62. Gene #20: 'amp_19p13.2' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	DEDIFFERENTIATED LIPOSARCOMA	DESMOID TUMOR	GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS	LEIOMYOSARCOMA (LMS)	MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)	MYXOFIBROSARCOMA	PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA	SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED	SYNOVIAL SARCOMA - BIPHASIC	SYNOVIAL SARCOMA - MONOPHASIC	UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
ALL	59	2	1	103	9	23	28	2	2	6	21
AMP PEAK 20(19P13.2) MUTATED	24	0	0	39	5	10	17	0	0	0	12
AMP PEAK 20(19P13.2) WILD-TYPE	35	2	1	64	4	13	11	2	2	6	9

Figure S62. Get High-res Image Gene #20: 'amp_19p13.2' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'amp_19q12' versus 'YEARS_TO_BIRTH'

P value = 0.000648 (Wilcoxon-test), Q value = 0.013

Table S63. Gene #21: 'amp_19q12' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
AMP PEAK 21(19Q12) MUTATED	92	64.8 (13.0)
AMP PEAK 21(19Q12) WILD-TYPE	163	58.8 (15.2)

Figure S63. Get High-res Image Gene #21: 'amp_19q12' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_19q12' versus 'RADIATION_THERAPY'

P value = 0.0404 (Fisher's exact test), Q value = 0.17

Table S64. Gene #21: 'amp_19q12' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	180	69
AMP PEAK 21(19Q12) MUTATED	58	32
AMP PEAK 21(19Q12) WILD-TYPE	122	37

Figure S64. Get High-res Image Gene #21: 'amp_19q12' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_19q12' versus 'HISTOLOGICAL_TYPE'

P value = 0.0117 (Fisher's exact test), Q value = 0.077

Table S65. Gene #21: 'amp_19q12' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	DEDIFFERENTIATED LIPOSARCOMA	DESMOID TUMOR	GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS	LEIOMYOSARCOMA (LMS)	MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)	MYXOFIBROSARCOMA	PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA	SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED	SYNOVIAL SARCOMA - BIPHASIC	SYNOVIAL SARCOMA - MONOPHASIC	UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
ALL	59	2	1	103	9	23	28	2	2	6	21
AMP PEAK 21(19Q12) MUTATED	18	0	0	32	3	14	16	0	0	0	10
AMP PEAK 21(19Q12) WILD-TYPE	41	2	1	71	6	9	12	2	2	6	11

Figure S65. Get High-res Image Gene #21: 'amp_19q12' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'amp_20q13.33' versus 'Time to Death'

P value = 0.031 (logrank test), Q value = 0.14

Table S66. Gene #22: 'amp_20q13.33' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	256	94	0.5 - 188.2 (26.4)
AMP PEAK 22(20Q13.33) MUTATED	98	42	0.6 - 143.4 (23.1)
AMP PEAK 22(20Q13.33) WILD-TYPE	158	52	0.5 - 188.2 (31.4)

Figure S66. Get High-res Image Gene #22: 'amp_20q13.33' versus Clinical Feature #1: 'Time to Death'

'amp_20q13.33' versus 'YEARS_TO_BIRTH'

P value = 0.000278 (Wilcoxon-test), Q value = 0.0075

Table S67. Gene #22: 'amp_20q13.33' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
AMP PEAK 22(20Q13.33) MUTATED	98	65.2 (13.4)
AMP PEAK 22(20Q13.33) WILD-TYPE	157	58.3 (14.9)

Figure S67. Get High-res Image Gene #22: 'amp_20q13.33' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_20q13.33' versus 'TUMOR_TISSUE_SITE'

P value = 0.0736 (Fisher's exact test), Q value = 0.24

Table S68. Gene #22: 'amp_20q13.33' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	CHEST - BREAST	CHEST - CHEST WALL	CHEST - LUNG/PLEURA	CHEST - MEDIASTINUM	CHEST - OTHER (PLEASE SPECIFY	GYNECOLOGICAL - OVARY	GYNECOLOGICAL - UTERUS	HEAD AND NECK - HEAD	HEAD AND NECK - NECK	HEAD AND NECK - OTHER (PLEASE SPECIFY	LOWER ABDOMINAL/PELVIC - BLADDER	LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY	LOWER ABDOMINAL/PELVIC - PELVIC	LOWER ABDOMINAL/PELVIC - SPERMATIC CORD	LOWER EXTREMITY - FOOT/ANKLE	LOWER EXTREMITY - GROIN	LOWER EXTREMITY - LOWER LEG/CALF	LOWER EXTREMITY - OTHER (PLEASE SPECIFY	LOWER EXTREMITY - THIGH/KNEE	RETROPERITONEUM/UPPER ABDOMINAL - COLON	RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC	RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL	RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY	RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY	RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS	RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM	RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES	SUPERFICIAL TRUNK - ABDOMINAL WALL	SUPERFICIAL TRUNK - BACK	SUPERFICIAL TRUNK - BUTTOCK	SUPERFICIAL TRUNK - FLANK	UPPER EXTREMITY - SHOULDER/AXILLA	UPPER EXTREMITY - UPPER ARM/ELBOW
ALL	1	7	2	1	2	1	28	2	1	2	1	2	10	2	4	2	17	5	43	4	2	5	8	2	1	73	3	2	5	4	1	7	5
AMP PEAK 22(20Q13.33) MUTATED	0	2	0	0	1	0	8	1	0	0	0	1	3	0	2	0	8	5	23	0	0	0	2	0	1	28	0	2	2	1	0	5	2
AMP PEAK 22(20Q13.33) WILD-TYPE	1	5	2	1	1	1	20	1	1	2	1	1	7	2	2	2	9	0	20	4	2	5	6	2	0	45	3	0	3	3	1	2	3

Figure S68. Get High-res Image Gene #22: 'amp_20q13.33' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'amp_20q13.33' versus 'GENDER'

P value = 0.0099 (Fisher's exact test), Q value = 0.068

Table S69. Gene #22: 'amp_20q13.33' versus Clinical Feature #4: 'GENDER'

nPatients	FEMALE	MALE
ALL	139	117
AMP PEAK 22(20Q13.33) MUTATED	43	55
AMP PEAK 22(20Q13.33) WILD-TYPE	96	62

Figure S69. Get High-res Image Gene #22: 'amp_20q13.33' versus Clinical Feature #4: 'GENDER'

'amp_20q13.33' versus 'RADIATION_THERAPY'

P value = 0.0134 (Fisher's exact test), Q value = 0.083

Table S70. Gene #22: 'amp_20q13.33' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	180	69
AMP PEAK 22(20Q13.33) MUTATED	60	35
AMP PEAK 22(20Q13.33) WILD-TYPE	120	34

Figure S70. Get High-res Image Gene #22: 'amp_20q13.33' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_20q13.33' versus 'HISTOLOGICAL_TYPE'

P value = 0.00099 (Fisher's exact test), Q value = 0.015

Table S71. Gene #22: 'amp_20q13.33' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	DEDIFFERENTIATED LIPOSARCOMA	DESMOID TUMOR	GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS	LEIOMYOSARCOMA (LMS)	MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)	MYXOFIBROSARCOMA	PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA	SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED	SYNOVIAL SARCOMA - BIPHASIC	SYNOVIAL SARCOMA - MONOPHASIC	UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
ALL	59	2	1	103	9	23	28	2	2	6	21
AMP PEAK 22(20Q13.33) MUTATED	21	0	0	29	5	14	17	0	0	0	12
AMP PEAK 22(20Q13.33) WILD-TYPE	38	2	1	74	4	9	11	2	2	6	9

Figure S71. Get High-res Image Gene #22: 'amp_20q13.33' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'amp_21q21.1' versus 'YEARS_TO_BIRTH'

P value = 0.00554 (Wilcoxon-test), Q value = 0.046

Table S72. Gene #23: 'amp_21q21.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
AMP PEAK 23(21Q21.1) MUTATED	72	64.9 (11.7)
AMP PEAK 23(21Q21.1) WILD-TYPE	183	59.4 (15.5)

Figure S72. Get High-res Image Gene #23: 'amp_21q21.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_21q21.1' versus 'GENDER'

P value = 0.0719 (Fisher's exact test), Q value = 0.24

Table S73. Gene #23: 'amp_21q21.1' versus Clinical Feature #4: 'GENDER'

nPatients	FEMALE	MALE
ALL	139	117
AMP PEAK 23(21Q21.1) MUTATED	33	40
AMP PEAK 23(21Q21.1) WILD-TYPE	106	77

Figure S73. Get High-res Image Gene #23: 'amp_21q21.1' versus Clinical Feature #4: 'GENDER'

'amp_xp21.2' versus 'YEARS_TO_BIRTH'

P value = 0.0346 (Wilcoxon-test), Q value = 0.15

Table S74. Gene #24: 'amp_xp21.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
AMP PEAK 24(XP21.2) MUTATED	96	63.6 (12.7)
AMP PEAK 24(XP21.2) WILD-TYPE	159	59.3 (15.6)

Figure S74. Get High-res Image Gene #24: 'amp_xp21.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_xp21.2' versus 'RADIATION_THERAPY'

P value = 0.0292 (Fisher's exact test), Q value = 0.14

Table S75. Gene #24: 'amp_xp21.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	180	69
AMP PEAK 24(XP21.2) MUTATED	61	34
AMP PEAK 24(XP21.2) WILD-TYPE	119	35

Figure S75. Get High-res Image Gene #24: 'amp_xp21.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_xp21.2' versus 'HISTOLOGICAL_TYPE'

P value = 0.00716 (Fisher's exact test), Q value = 0.056

Table S76. Gene #24: 'amp_xp21.2' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	DEDIFFERENTIATED LIPOSARCOMA	DESMOID TUMOR	GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS	LEIOMYOSARCOMA (LMS)	MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)	MYXOFIBROSARCOMA	PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA	SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED	SYNOVIAL SARCOMA - BIPHASIC	SYNOVIAL SARCOMA - MONOPHASIC	UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
ALL	59	2	1	103	9	23	28	2	2	6	21
AMP PEAK 24(XP21.2) MUTATED	17	0	0	40	1	12	13	0	0	0	14
AMP PEAK 24(XP21.2) WILD-TYPE	42	2	1	63	8	11	15	2	2	6	7

Figure S76. Get High-res Image Gene #24: 'amp_xp21.2' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'amp_xq21.1' versus 'YEARS_TO_BIRTH'

P value = 0.0544 (Wilcoxon-test), Q value = 0.2

Table S77. Gene #25: 'amp_xq21.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
AMP PEAK 25(XQ21.1) MUTATED	46	64.5 (12.2)
AMP PEAK 25(XQ21.1) WILD-TYPE	209	60.1 (15.1)

Figure S77. Get High-res Image Gene #25: 'amp_xq21.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_1p36.32' versus 'Time to Death'

P value = 0.0369 (logrank test), Q value = 0.16

Table S78. Gene #26: 'del_1p36.32' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	256	94	0.5 - 188.2 (26.4)
DEL PEAK 1(1P36.32) MUTATED	69	22	0.7 - 188.2 (35.3)
DEL PEAK 1(1P36.32) WILD-TYPE	187	72	0.5 - 135.5 (24.6)

Figure S78. Get High-res Image Gene #26: 'del_1p36.32' versus Clinical Feature #1: 'Time to Death'

'del_1p36.32' versus 'GENDER'

P value = 0.000399 (Fisher's exact test), Q value = 0.0095

Table S79. Gene #26: 'del_1p36.32' versus Clinical Feature #4: 'GENDER'

nPatients	FEMALE	MALE
ALL	139	117
DEL PEAK 1(1P36.32) MUTATED	50	19
DEL PEAK 1(1P36.32) WILD-TYPE	89	98

Figure S79. Get High-res Image Gene #26: 'del_1p36.32' versus Clinical Feature #4: 'GENDER'

'del_1p36.32' versus 'RADIATION_THERAPY'

P value = 0.00979 (Fisher's exact test), Q value = 0.068

Table S80. Gene #26: 'del_1p36.32' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	180	69
DEL PEAK 1(1P36.32) MUTATED	56	10
DEL PEAK 1(1P36.32) WILD-TYPE	124	59

Figure S80. Get High-res Image Gene #26: 'del_1p36.32' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_1p36.32' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00054

Table S81. Gene #26: 'del_1p36.32' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	DEDIFFERENTIATED LIPOSARCOMA	DESMOID TUMOR	GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS	LEIOMYOSARCOMA (LMS)	MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)	MYXOFIBROSARCOMA	PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA	SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED	SYNOVIAL SARCOMA - BIPHASIC	SYNOVIAL SARCOMA - MONOPHASIC	UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
ALL	59	2	1	103	9	23	28	2	2	6	21
DEL PEAK 1(1P36.32) MUTATED	5	0	0	51	3	4	4	0	0	1	1
DEL PEAK 1(1P36.32) WILD-TYPE	54	2	1	52	6	19	24	2	2	5	20

Figure S81. Get High-res Image Gene #26: 'del_1p36.32' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_1q44' versus 'YEARS_TO_BIRTH'

P value = 0.00233 (Wilcoxon-test), Q value = 0.027

Table S82. Gene #27: 'del_1q44' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
DEL PEAK 2(1Q44) MUTATED	80	65.0 (13.5)
DEL PEAK 2(1Q44) WILD-TYPE	175	59.1 (14.8)

Figure S82. Get High-res Image Gene #27: 'del_1q44' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_1q44' versus 'RADIATION_THERAPY'

P value = 0.000746 (Fisher's exact test), Q value = 0.014

Table S83. Gene #27: 'del_1q44' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	180	69
DEL PEAK 2(1Q44) MUTATED	45	33
DEL PEAK 2(1Q44) WILD-TYPE	135	36

Figure S83. Get High-res Image Gene #27: 'del_1q44' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_1q44' versus 'HISTOLOGICAL_TYPE'

P value = 5e-05 (Fisher's exact test), Q value = 0.0019

Table S84. Gene #27: 'del_1q44' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	DEDIFFERENTIATED LIPOSARCOMA	DESMOID TUMOR	GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS	LEIOMYOSARCOMA (LMS)	MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)	MYXOFIBROSARCOMA	PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA	SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED	SYNOVIAL SARCOMA - BIPHASIC	SYNOVIAL SARCOMA - MONOPHASIC	UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
ALL	59	2	1	103	9	23	28	2	2	6	21
DEL PEAK 2(1Q44) MUTATED	19	0	0	18	4	10	16	0	0	0	13
DEL PEAK 2(1Q44) WILD-TYPE	40	2	1	85	5	13	12	2	2	6	8

Figure S84. Get High-res Image Gene #27: 'del_1q44' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_2p25.3' versus 'YEARS_TO_BIRTH'

P value = 0.0642 (Wilcoxon-test), Q value = 0.22

Table S85. Gene #28: 'del_2p25.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
DEL PEAK 3(2P25.3) MUTATED	93	63.5 (13.8)
DEL PEAK 3(2P25.3) WILD-TYPE	162	59.5 (15.0)

Figure S85. Get High-res Image Gene #28: 'del_2p25.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_2p25.3' versus 'GENDER'

P value = 0.0267 (Fisher's exact test), Q value = 0.13

Table S86. Gene #28: 'del_2p25.3' versus Clinical Feature #4: 'GENDER'

nPatients	FEMALE	MALE
ALL	139	117
DEL PEAK 3(2P25.3) MUTATED	60	34
DEL PEAK 3(2P25.3) WILD-TYPE	79	83

Figure S86. Get High-res Image Gene #28: 'del_2p25.3' versus Clinical Feature #4: 'GENDER'

'del_2p25.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.00142 (Fisher's exact test), Q value = 0.019

Table S87. Gene #28: 'del_2p25.3' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	DEDIFFERENTIATED LIPOSARCOMA	DESMOID TUMOR	GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS	LEIOMYOSARCOMA (LMS)	MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)	MYXOFIBROSARCOMA	PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA	SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED	SYNOVIAL SARCOMA - BIPHASIC	SYNOVIAL SARCOMA - MONOPHASIC	UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
ALL	59	2	1	103	9	23	28	2	2	6	21
DEL PEAK 3(2P25.3) MUTATED	10	0	0	48	3	12	13	0	0	0	8
DEL PEAK 3(2P25.3) WILD-TYPE	49	2	1	55	6	11	15	2	2	6	13

Figure S87. Get High-res Image Gene #28: 'del_2p25.3' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_2p25.3' versus 'RACE'

P value = 0.00249 (Fisher's exact test), Q value = 0.028

Table S88. Gene #28: 'del_2p25.3' versus Clinical Feature #8: 'RACE'

nPatients	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	6	18	223
DEL PEAK 3(2P25.3) MUTATED	1	13	75
DEL PEAK 3(2P25.3) WILD-TYPE	5	5	148

Figure S88. Get High-res Image Gene #28: 'del_2p25.3' versus Clinical Feature #8: 'RACE'

'del_2q37.3' versus 'Time to Death'

P value = 0.0107 (logrank test), Q value = 0.072

Table S89. Gene #29: 'del_2q37.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	256	94	0.5 - 188.2 (26.4)
DEL PEAK 4(2Q37.3) MUTATED	108	49	1.1 - 106.5 (23.9)
DEL PEAK 4(2Q37.3) WILD-TYPE	148	45	0.5 - 188.2 (29.7)

Figure S89. Get High-res Image Gene #29: 'del_2q37.3' versus Clinical Feature #1: 'Time to Death'

'del_2q37.3' versus 'YEARS_TO_BIRTH'

P value = 0.00887 (Wilcoxon-test), Q value = 0.066

Table S90. Gene #29: 'del_2q37.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
DEL PEAK 4(2Q37.3) MUTATED	107	63.8 (13.9)
DEL PEAK 4(2Q37.3) WILD-TYPE	148	58.9 (14.9)

Figure S90. Get High-res Image Gene #29: 'del_2q37.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_2q37.3' versus 'TUMOR_TISSUE_SITE'

P value = 0.025 (Fisher's exact test), Q value = 0.13

Table S91. Gene #29: 'del_2q37.3' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	CHEST - BREAST	CHEST - CHEST WALL	CHEST - LUNG/PLEURA	CHEST - MEDIASTINUM	CHEST - OTHER (PLEASE SPECIFY	GYNECOLOGICAL - OVARY	GYNECOLOGICAL - UTERUS	HEAD AND NECK - HEAD	HEAD AND NECK - NECK	HEAD AND NECK - OTHER (PLEASE SPECIFY	LOWER ABDOMINAL/PELVIC - BLADDER	LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY	LOWER ABDOMINAL/PELVIC - PELVIC	LOWER ABDOMINAL/PELVIC - SPERMATIC CORD	LOWER EXTREMITY - FOOT/ANKLE	LOWER EXTREMITY - GROIN	LOWER EXTREMITY - LOWER LEG/CALF	LOWER EXTREMITY - OTHER (PLEASE SPECIFY	LOWER EXTREMITY - THIGH/KNEE	RETROPERITONEUM/UPPER ABDOMINAL - COLON	RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC	RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL	RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY	RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY	RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS	RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM	RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES	SUPERFICIAL TRUNK - ABDOMINAL WALL	SUPERFICIAL TRUNK - BACK	SUPERFICIAL TRUNK - BUTTOCK	SUPERFICIAL TRUNK - FLANK	UPPER EXTREMITY - SHOULDER/AXILLA	UPPER EXTREMITY - UPPER ARM/ELBOW
ALL	1	7	2	1	2	1	28	2	1	2	1	2	10	2	4	2	17	5	43	4	2	5	8	2	1	73	3	2	5	4	1	7	5
DEL PEAK 4(2Q37.3) MUTATED	0	5	0	0	1	0	18	1	0	0	1	1	2	0	1	0	6	5	23	1	1	0	3	0	1	26	0	2	2	2	0	3	3
DEL PEAK 4(2Q37.3) WILD-TYPE	1	2	2	1	1	1	10	1	1	2	0	1	8	2	3	2	11	0	20	3	1	5	5	2	0	47	3	0	3	2	1	4	2

Figure S91. Get High-res Image Gene #29: 'del_2q37.3' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_2q37.3' versus 'RADIATION_THERAPY'

P value = 0.00987 (Fisher's exact test), Q value = 0.068

Table S92. Gene #29: 'del_2q37.3' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	180	69
DEL PEAK 4(2Q37.3) MUTATED	66	38
DEL PEAK 4(2Q37.3) WILD-TYPE	114	31

Figure S92. Get High-res Image Gene #29: 'del_2q37.3' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_2q37.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.00111 (Fisher's exact test), Q value = 0.016

Table S93. Gene #29: 'del_2q37.3' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	DEDIFFERENTIATED LIPOSARCOMA	DESMOID TUMOR	GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS	LEIOMYOSARCOMA (LMS)	MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)	MYXOFIBROSARCOMA	PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA	SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED	SYNOVIAL SARCOMA - BIPHASIC	SYNOVIAL SARCOMA - MONOPHASIC	UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
ALL	59	2	1	103	9	23	28	2	2	6	21
DEL PEAK 4(2Q37.3) MUTATED	17	0	0	45	2	15	18	0	0	0	11
DEL PEAK 4(2Q37.3) WILD-TYPE	42	2	1	58	7	8	10	2	2	6	10

Figure S93. Get High-res Image Gene #29: 'del_2q37.3' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_2q37.3' versus 'Time to Death'

P value = 0.0549 (logrank test), Q value = 0.2

Table S94. Gene #30: 'del_2q37.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	256	94	0.5 - 188.2 (26.4)
DEL PEAK 5(2Q37.3) MUTATED	110	48	1.1 - 143.4 (24.6)
DEL PEAK 5(2Q37.3) WILD-TYPE	146	46	0.5 - 188.2 (29.2)

Figure S94. Get High-res Image Gene #30: 'del_2q37.3' versus Clinical Feature #1: 'Time to Death'

'del_2q37.3' versus 'YEARS_TO_BIRTH'

P value = 0.00278 (Wilcoxon-test), Q value = 0.029

Table S95. Gene #30: 'del_2q37.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
DEL PEAK 5(2Q37.3) MUTATED	109	64.1 (13.9)
DEL PEAK 5(2Q37.3) WILD-TYPE	146	58.6 (14.8)

Figure S95. Get High-res Image Gene #30: 'del_2q37.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_2q37.3' versus 'TUMOR_TISSUE_SITE'

P value = 0.00588 (Fisher's exact test), Q value = 0.049

Table S96. Gene #30: 'del_2q37.3' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	CHEST - BREAST	CHEST - CHEST WALL	CHEST - LUNG/PLEURA	CHEST - MEDIASTINUM	CHEST - OTHER (PLEASE SPECIFY	GYNECOLOGICAL - OVARY	GYNECOLOGICAL - UTERUS	HEAD AND NECK - HEAD	HEAD AND NECK - NECK	HEAD AND NECK - OTHER (PLEASE SPECIFY	LOWER ABDOMINAL/PELVIC - BLADDER	LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY	LOWER ABDOMINAL/PELVIC - PELVIC	LOWER ABDOMINAL/PELVIC - SPERMATIC CORD	LOWER EXTREMITY - FOOT/ANKLE	LOWER EXTREMITY - GROIN	LOWER EXTREMITY - LOWER LEG/CALF	LOWER EXTREMITY - OTHER (PLEASE SPECIFY	LOWER EXTREMITY - THIGH/KNEE	RETROPERITONEUM/UPPER ABDOMINAL - COLON	RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC	RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL	RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY	RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY	RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS	RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM	RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES	SUPERFICIAL TRUNK - ABDOMINAL WALL	SUPERFICIAL TRUNK - BACK	SUPERFICIAL TRUNK - BUTTOCK	SUPERFICIAL TRUNK - FLANK	UPPER EXTREMITY - SHOULDER/AXILLA	UPPER EXTREMITY - UPPER ARM/ELBOW
ALL	1	7	2	1	2	1	28	2	1	2	1	2	10	2	4	2	17	5	43	4	2	5	8	2	1	73	3	2	5	4	1	7	5
DEL PEAK 5(2Q37.3) MUTATED	0	4	0	0	1	1	20	1	0	0	0	1	2	0	0	0	5	5	22	1	1	0	3	0	1	29	0	2	3	2	0	3	3
DEL PEAK 5(2Q37.3) WILD-TYPE	1	3	2	1	1	0	8	1	1	2	1	1	8	2	4	2	12	0	21	3	1	5	5	2	0	44	3	0	2	2	1	4	2

Figure S96. Get High-res Image Gene #30: 'del_2q37.3' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_2q37.3' versus 'RADIATION_THERAPY'

P value = 0.0638 (Fisher's exact test), Q value = 0.22

Table S97. Gene #30: 'del_2q37.3' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	180	69
DEL PEAK 5(2Q37.3) MUTATED	70	36
DEL PEAK 5(2Q37.3) WILD-TYPE	110	33

Figure S97. Get High-res Image Gene #30: 'del_2q37.3' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_2q37.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.0038 (Fisher's exact test), Q value = 0.035

Table S98. Gene #30: 'del_2q37.3' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	DEDIFFERENTIATED LIPOSARCOMA	DESMOID TUMOR	GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS	LEIOMYOSARCOMA (LMS)	MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)	MYXOFIBROSARCOMA	PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA	SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED	SYNOVIAL SARCOMA - BIPHASIC	SYNOVIAL SARCOMA - MONOPHASIC	UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
ALL	59	2	1	103	9	23	28	2	2	6	21
DEL PEAK 5(2Q37.3) MUTATED	19	0	0	45	2	15	17	0	0	0	12
DEL PEAK 5(2Q37.3) WILD-TYPE	40	2	1	58	7	8	11	2	2	6	9

Figure S98. Get High-res Image Gene #30: 'del_2q37.3' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_3p21.31' versus 'RADIATION_THERAPY'

P value = 0.0757 (Fisher's exact test), Q value = 0.25

Table S99. Gene #31: 'del_3p21.31' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	180	69
DEL PEAK 6(3P21.31) MUTATED	40	23
DEL PEAK 6(3P21.31) WILD-TYPE	140	46

Figure S99. Get High-res Image Gene #31: 'del_3p21.31' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_3p21.31' versus 'HISTOLOGICAL_TYPE'

P value = 0.00095 (Fisher's exact test), Q value = 0.015

Table S100. Gene #31: 'del_3p21.31' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	DEDIFFERENTIATED LIPOSARCOMA	DESMOID TUMOR	GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS	LEIOMYOSARCOMA (LMS)	MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)	MYXOFIBROSARCOMA	PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA	SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED	SYNOVIAL SARCOMA - BIPHASIC	SYNOVIAL SARCOMA - MONOPHASIC	UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
ALL	59	2	1	103	9	23	28	2	2	6	21
DEL PEAK 6(3P21.31) MUTATED	12	0	0	15	3	11	12	0	2	3	7
DEL PEAK 6(3P21.31) WILD-TYPE	47	2	1	88	6	12	16	2	0	3	14

Figure S100. Get High-res Image Gene #31: 'del_3p21.31' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_3q13.31' versus 'YEARS_TO_BIRTH'

P value = 0.0123 (Wilcoxon-test), Q value = 0.08

Table S101. Gene #32: 'del_3q13.31' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
DEL PEAK 7(3Q13.31) MUTATED	50	64.7 (16.0)
DEL PEAK 7(3Q13.31) WILD-TYPE	205	60.0 (14.2)

Figure S101. Get High-res Image Gene #32: 'del_3q13.31' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_3q13.31' versus 'RADIATION_THERAPY'

P value = 0.014 (Fisher's exact test), Q value = 0.085

Table S102. Gene #32: 'del_3q13.31' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	180	69
DEL PEAK 7(3Q13.31) MUTATED	29	21
DEL PEAK 7(3Q13.31) WILD-TYPE	151	48

Figure S102. Get High-res Image Gene #32: 'del_3q13.31' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_4q35.1' versus 'YEARS_TO_BIRTH'

P value = 0.00202 (Wilcoxon-test), Q value = 0.024

Table S103. Gene #34: 'del_4q35.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
DEL PEAK 9(4Q35.1) MUTATED	93	64.5 (15.0)
DEL PEAK 9(4Q35.1) WILD-TYPE	162	58.9 (14.2)

Figure S103. Get High-res Image Gene #34: 'del_4q35.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_4q35.1' versus 'RADIATION_THERAPY'

P value = 0.00516 (Fisher's exact test), Q value = 0.044

Table S104. Gene #34: 'del_4q35.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	180	69
DEL PEAK 9(4Q35.1) MUTATED	56	35
DEL PEAK 9(4Q35.1) WILD-TYPE	124	34

Figure S104. Get High-res Image Gene #34: 'del_4q35.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_4q35.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.00765 (Fisher's exact test), Q value = 0.058

Table S105. Gene #34: 'del_4q35.1' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	DEDIFFERENTIATED LIPOSARCOMA	DESMOID TUMOR	GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS	LEIOMYOSARCOMA (LMS)	MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)	MYXOFIBROSARCOMA	PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA	SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED	SYNOVIAL SARCOMA - BIPHASIC	SYNOVIAL SARCOMA - MONOPHASIC	UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
ALL	59	2	1	103	9	23	28	2	2	6	21
DEL PEAK 9(4Q35.1) MUTATED	17	0	0	34	4	15	16	0	0	0	8
DEL PEAK 9(4Q35.1) WILD-TYPE	42	2	1	69	5	8	12	2	2	6	13

Figure S105. Get High-res Image Gene #34: 'del_4q35.1' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_5p15.33' versus 'TUMOR_TISSUE_SITE'

P value = 0.0372 (Fisher's exact test), Q value = 0.16

Table S106. Gene #35: 'del_5p15.33' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	CHEST - BREAST	CHEST - CHEST WALL	CHEST - LUNG/PLEURA	CHEST - MEDIASTINUM	CHEST - OTHER (PLEASE SPECIFY	GYNECOLOGICAL - OVARY	GYNECOLOGICAL - UTERUS	HEAD AND NECK - HEAD	HEAD AND NECK - NECK	HEAD AND NECK - OTHER (PLEASE SPECIFY	LOWER ABDOMINAL/PELVIC - BLADDER	LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY	LOWER ABDOMINAL/PELVIC - PELVIC	LOWER ABDOMINAL/PELVIC - SPERMATIC CORD	LOWER EXTREMITY - FOOT/ANKLE	LOWER EXTREMITY - GROIN	LOWER EXTREMITY - LOWER LEG/CALF	LOWER EXTREMITY - OTHER (PLEASE SPECIFY	LOWER EXTREMITY - THIGH/KNEE	RETROPERITONEUM/UPPER ABDOMINAL - COLON	RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC	RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL	RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY	RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY	RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS	RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM	RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES	SUPERFICIAL TRUNK - ABDOMINAL WALL	SUPERFICIAL TRUNK - BACK	SUPERFICIAL TRUNK - BUTTOCK	SUPERFICIAL TRUNK - FLANK	UPPER EXTREMITY - SHOULDER/AXILLA	UPPER EXTREMITY - UPPER ARM/ELBOW
ALL	1	7	2	1	2	1	28	2	1	2	1	2	10	2	4	2	17	5	43	4	2	5	8	2	1	73	3	2	5	4	1	7	5
DEL PEAK 10(5P15.33) MUTATED	1	4	0	0	0	0	2	0	0	0	0	0	0	0	1	1	2	2	6	0	1	0	1	0	0	6	0	1	1	2	0	0	2
DEL PEAK 10(5P15.33) WILD-TYPE	0	3	2	1	2	1	26	2	1	2	1	2	10	2	3	1	15	3	37	4	1	5	7	2	1	67	3	1	4	2	1	7	3

Figure S106. Get High-res Image Gene #35: 'del_5p15.33' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_6p25.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.0341 (Fisher's exact test), Q value = 0.15

Table S107. Gene #36: 'del_6p25.3' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	DEDIFFERENTIATED LIPOSARCOMA	DESMOID TUMOR	GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS	LEIOMYOSARCOMA (LMS)	MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)	MYXOFIBROSARCOMA	PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA	SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED	SYNOVIAL SARCOMA - BIPHASIC	SYNOVIAL SARCOMA - MONOPHASIC	UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
ALL	59	2	1	103	9	23	28	2	2	6	21
DEL PEAK 11(6P25.3) MUTATED	11	1	0	45	4	7	7	0	0	0	6
DEL PEAK 11(6P25.3) WILD-TYPE	48	1	1	58	5	16	21	2	2	6	15

Figure S107. Get High-res Image Gene #36: 'del_6p25.3' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_6q14.1' versus 'TUMOR_TISSUE_SITE'

P value = 0.0231 (Fisher's exact test), Q value = 0.12

Table S108. Gene #37: 'del_6q14.1' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	CHEST - BREAST	CHEST - CHEST WALL	CHEST - LUNG/PLEURA	CHEST - MEDIASTINUM	CHEST - OTHER (PLEASE SPECIFY	GYNECOLOGICAL - OVARY	GYNECOLOGICAL - UTERUS	HEAD AND NECK - HEAD	HEAD AND NECK - NECK	HEAD AND NECK - OTHER (PLEASE SPECIFY	LOWER ABDOMINAL/PELVIC - BLADDER	LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY	LOWER ABDOMINAL/PELVIC - PELVIC	LOWER ABDOMINAL/PELVIC - SPERMATIC CORD	LOWER EXTREMITY - FOOT/ANKLE	LOWER EXTREMITY - GROIN	LOWER EXTREMITY - LOWER LEG/CALF	LOWER EXTREMITY - OTHER (PLEASE SPECIFY	LOWER EXTREMITY - THIGH/KNEE	RETROPERITONEUM/UPPER ABDOMINAL - COLON	RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC	RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL	RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY	RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY	RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS	RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM	RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES	SUPERFICIAL TRUNK - ABDOMINAL WALL	SUPERFICIAL TRUNK - BACK	SUPERFICIAL TRUNK - BUTTOCK	SUPERFICIAL TRUNK - FLANK	UPPER EXTREMITY - SHOULDER/AXILLA	UPPER EXTREMITY - UPPER ARM/ELBOW
ALL	1	7	2	1	2	1	28	2	1	2	1	2	10	2	4	2	17	5	43	4	2	5	8	2	1	73	3	2	5	4	1	7	5
DEL PEAK 12(6Q14.1) MUTATED	1	3	0	1	1	0	3	1	0	0	0	1	3	0	2	0	10	4	17	1	1	0	1	1	1	18	2	0	2	1	0	2	0
DEL PEAK 12(6Q14.1) WILD-TYPE	0	4	2	0	1	1	25	1	1	2	1	1	7	2	2	2	7	1	26	3	1	5	7	1	0	55	1	2	3	3	1	5	5

Figure S108. Get High-res Image Gene #37: 'del_6q14.1' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_6q14.1' versus 'RADIATION_THERAPY'

P value = 0.0206 (Fisher's exact test), Q value = 0.11

Table S109. Gene #37: 'del_6q14.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	180	69
DEL PEAK 12(6Q14.1) MUTATED	47	29
DEL PEAK 12(6Q14.1) WILD-TYPE	133	40

Figure S109. Get High-res Image Gene #37: 'del_6q14.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_8p23.3' versus 'YEARS_TO_BIRTH'

P value = 0.0486 (Wilcoxon-test), Q value = 0.19

Table S110. Gene #39: 'del_8p23.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
DEL PEAK 14(8P23.3) MUTATED	81	63.7 (13.3)
DEL PEAK 14(8P23.3) WILD-TYPE	174	59.6 (15.2)

Figure S110. Get High-res Image Gene #39: 'del_8p23.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_8p23.3' versus 'RADIATION_THERAPY'

P value = 0.0511 (Fisher's exact test), Q value = 0.2

Table S111. Gene #39: 'del_8p23.3' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	180	69
DEL PEAK 14(8P23.3) MUTATED	52	29
DEL PEAK 14(8P23.3) WILD-TYPE	128	40

Figure S111. Get High-res Image Gene #39: 'del_8p23.3' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_9p24.3' versus 'YEARS_TO_BIRTH'

P value = 0.00146 (Wilcoxon-test), Q value = 0.019

Table S112. Gene #40: 'del_9p24.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
DEL PEAK 15(9P24.3) MUTATED	100	64.8 (12.7)
DEL PEAK 15(9P24.3) WILD-TYPE	155	58.5 (15.4)

Figure S112. Get High-res Image Gene #40: 'del_9p24.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_9p21.3' versus 'Time to Death'

P value = 0.0538 (logrank test), Q value = 0.2

Table S113. Gene #41: 'del_9p21.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	256	94	0.5 - 188.2 (26.4)
DEL PEAK 16(9P21.3) MUTATED	114	49	0.6 - 188.2 (24.3)
DEL PEAK 16(9P21.3) WILD-TYPE	142	45	0.5 - 135.5 (28.6)

Figure S113. Get High-res Image Gene #41: 'del_9p21.3' versus Clinical Feature #1: 'Time to Death'

'del_9p21.3' versus 'YEARS_TO_BIRTH'

P value = 0.00193 (Wilcoxon-test), Q value = 0.024

Table S114. Gene #41: 'del_9p21.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
DEL PEAK 16(9P21.3) MUTATED	114	64.2 (13.2)
DEL PEAK 16(9P21.3) WILD-TYPE	141	58.3 (15.3)

Figure S114. Get High-res Image Gene #41: 'del_9p21.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_9p21.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.0268 (Fisher's exact test), Q value = 0.13

Table S115. Gene #41: 'del_9p21.3' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	DEDIFFERENTIATED LIPOSARCOMA	DESMOID TUMOR	GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS	LEIOMYOSARCOMA (LMS)	MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)	MYXOFIBROSARCOMA	PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA	SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED	SYNOVIAL SARCOMA - BIPHASIC	SYNOVIAL SARCOMA - MONOPHASIC	UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
ALL	59	2	1	103	9	23	28	2	2	6	21
DEL PEAK 16(9P21.3) MUTATED	25	0	0	39	7	12	17	0	0	1	13
DEL PEAK 16(9P21.3) WILD-TYPE	34	2	1	64	2	11	11	2	2	5	8

Figure S115. Get High-res Image Gene #41: 'del_9p21.3' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_9q34.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.00067 (Fisher's exact test), Q value = 0.013

Table S116. Gene #42: 'del_9q34.3' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	DEDIFFERENTIATED LIPOSARCOMA	DESMOID TUMOR	GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS	LEIOMYOSARCOMA (LMS)	MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)	MYXOFIBROSARCOMA	PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA	SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED	SYNOVIAL SARCOMA - BIPHASIC	SYNOVIAL SARCOMA - MONOPHASIC	UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
ALL	59	2	1	103	9	23	28	2	2	6	21
DEL PEAK 17(9Q34.3) MUTATED	3	0	0	36	2	9	5	0	0	0	6
DEL PEAK 17(9Q34.3) WILD-TYPE	56	2	1	67	7	14	23	2	2	6	15

Figure S116. Get High-res Image Gene #42: 'del_9q34.3' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_9q34.3' versus 'RESIDUAL_TUMOR'

P value = 0.00282 (Fisher's exact test), Q value = 0.029

Table S117. Gene #42: 'del_9q34.3' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	152	68	9	26
DEL PEAK 17(9Q34.3) MUTATED	37	12	7	5
DEL PEAK 17(9Q34.3) WILD-TYPE	115	56	2	21

Figure S117. Get High-res Image Gene #42: 'del_9q34.3' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'del_9q34.3' versus 'RACE'

P value = 0.0176 (Fisher's exact test), Q value = 0.1

Table S118. Gene #42: 'del_9q34.3' versus Clinical Feature #8: 'RACE'

nPatients	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	6	18	223
DEL PEAK 17(9Q34.3) MUTATED	1	9	45
DEL PEAK 17(9Q34.3) WILD-TYPE	5	9	178

Figure S118. Get High-res Image Gene #42: 'del_9q34.3' versus Clinical Feature #8: 'RACE'

'del_10p15.3' versus 'YEARS_TO_BIRTH'

P value = 0.0285 (Wilcoxon-test), Q value = 0.14

Table S119. Gene #43: 'del_10p15.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
DEL PEAK 18(10P15.3) MUTATED	127	62.8 (13.9)
DEL PEAK 18(10P15.3) WILD-TYPE	128	59.1 (15.2)

Figure S119. Get High-res Image Gene #43: 'del_10p15.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_10p15.3' versus 'HISTOLOGICAL_TYPE'

P value = 7e-05 (Fisher's exact test), Q value = 0.0023

Table S120. Gene #43: 'del_10p15.3' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	DEDIFFERENTIATED LIPOSARCOMA	DESMOID TUMOR	GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS	LEIOMYOSARCOMA (LMS)	MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)	MYXOFIBROSARCOMA	PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA	SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED	SYNOVIAL SARCOMA - BIPHASIC	SYNOVIAL SARCOMA - MONOPHASIC	UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
ALL	59	2	1	103	9	23	28	2	2	6	21
DEL PEAK 18(10P15.3) MUTATED	17	0	0	63	6	14	12	0	0	1	15
DEL PEAK 18(10P15.3) WILD-TYPE	42	2	1	40	3	9	16	2	2	5	6

Figure S120. Get High-res Image Gene #43: 'del_10p15.3' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_10q23.31' versus 'YEARS_TO_BIRTH'

P value = 0.0204 (Wilcoxon-test), Q value = 0.11

Table S121. Gene #44: 'del_10q23.31' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
DEL PEAK 19(10Q23.31) MUTATED	138	63.1 (13.0)
DEL PEAK 19(10Q23.31) WILD-TYPE	117	58.4 (16.2)

Figure S121. Get High-res Image Gene #44: 'del_10q23.31' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_10q23.31' versus 'RADIATION_THERAPY'

P value = 0.0476 (Fisher's exact test), Q value = 0.19

Table S122. Gene #44: 'del_10q23.31' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	180	69
DEL PEAK 19(10Q23.31) MUTATED	89	44
DEL PEAK 19(10Q23.31) WILD-TYPE	91	25

Figure S122. Get High-res Image Gene #44: 'del_10q23.31' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_10q23.31' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00054

Table S123. Gene #44: 'del_10q23.31' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	DEDIFFERENTIATED LIPOSARCOMA	DESMOID TUMOR	GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS	LEIOMYOSARCOMA (LMS)	MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)	MYXOFIBROSARCOMA	PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA	SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED	SYNOVIAL SARCOMA - BIPHASIC	SYNOVIAL SARCOMA - MONOPHASIC	UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
ALL	59	2	1	103	9	23	28	2	2	6	21
DEL PEAK 19(10Q23.31) MUTATED	10	0	0	79	4	14	16	0	0	0	15
DEL PEAK 19(10Q23.31) WILD-TYPE	49	2	1	24	5	9	12	2	2	6	6

Figure S123. Get High-res Image Gene #44: 'del_10q23.31' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_10q23.31' versus 'RACE'

P value = 0.0168 (Fisher's exact test), Q value = 0.099

Table S124. Gene #44: 'del_10q23.31' versus Clinical Feature #8: 'RACE'

nPatients	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	6	18	223
DEL PEAK 19(10Q23.31) MUTATED	2	15	116
DEL PEAK 19(10Q23.31) WILD-TYPE	4	3	107

Figure S124. Get High-res Image Gene #44: 'del_10q23.31' versus Clinical Feature #8: 'RACE'

'del_10q26.3' versus 'YEARS_TO_BIRTH'

P value = 0.00294 (Wilcoxon-test), Q value = 0.03

Table S125. Gene #45: 'del_10q26.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
DEL PEAK 20(10Q26.3) MUTATED	131	63.8 (12.7)
DEL PEAK 20(10Q26.3) WILD-TYPE	124	57.9 (16.0)

Figure S125. Get High-res Image Gene #45: 'del_10q26.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_10q26.3' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00054

Table S126. Gene #45: 'del_10q26.3' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	DEDIFFERENTIATED LIPOSARCOMA	DESMOID TUMOR	GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS	LEIOMYOSARCOMA (LMS)	MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)	MYXOFIBROSARCOMA	PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA	SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED	SYNOVIAL SARCOMA - BIPHASIC	SYNOVIAL SARCOMA - MONOPHASIC	UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
ALL	59	2	1	103	9	23	28	2	2	6	21
DEL PEAK 20(10Q26.3) MUTATED	9	0	0	77	3	14	14	0	0	0	15
DEL PEAK 20(10Q26.3) WILD-TYPE	50	2	1	26	6	9	14	2	2	6	6

Figure S126. Get High-res Image Gene #45: 'del_10q26.3' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_10q26.3' versus 'RACE'

P value = 0.0699 (Fisher's exact test), Q value = 0.24

Table S127. Gene #45: 'del_10q26.3' versus Clinical Feature #8: 'RACE'

nPatients	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	6	18	223
DEL PEAK 20(10Q26.3) MUTATED	3	14	110
DEL PEAK 20(10Q26.3) WILD-TYPE	3	4	113

Figure S127. Get High-res Image Gene #45: 'del_10q26.3' versus Clinical Feature #8: 'RACE'

'del_11p15.5' versus 'YEARS_TO_BIRTH'

P value = 0.00413 (Wilcoxon-test), Q value = 0.037

Table S128. Gene #46: 'del_11p15.5' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
DEL PEAK 21(11P15.5) MUTATED	109	63.8 (14.2)
DEL PEAK 21(11P15.5) WILD-TYPE	146	58.8 (14.7)

Figure S128. Get High-res Image Gene #46: 'del_11p15.5' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_11p15.5' versus 'RADIATION_THERAPY'

P value = 0.0467 (Fisher's exact test), Q value = 0.19

Table S129. Gene #46: 'del_11p15.5' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	180	69
DEL PEAK 21(11P15.5) MUTATED	71	37
DEL PEAK 21(11P15.5) WILD-TYPE	109	32

Figure S129. Get High-res Image Gene #46: 'del_11p15.5' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_11q24.2' versus 'YEARS_TO_BIRTH'

P value = 0.0127 (Wilcoxon-test), Q value = 0.081

Table S130. Gene #47: 'del_11q24.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
DEL PEAK 22(11Q24.2) MUTATED	122	63.3 (13.6)
DEL PEAK 22(11Q24.2) WILD-TYPE	133	58.7 (15.3)

Figure S130. Get High-res Image Gene #47: 'del_11q24.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_11q24.2' versus 'RADIATION_THERAPY'

P value = 0.0231 (Fisher's exact test), Q value = 0.12

Table S131. Gene #47: 'del_11q24.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	180	69
DEL PEAK 22(11Q24.2) MUTATED	79	42
DEL PEAK 22(11Q24.2) WILD-TYPE	101	27

Figure S131. Get High-res Image Gene #47: 'del_11q24.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_11q24.2' versus 'HISTOLOGICAL_TYPE'

P value = 0.00897 (Fisher's exact test), Q value = 0.066

Table S132. Gene #47: 'del_11q24.2' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	DEDIFFERENTIATED LIPOSARCOMA	DESMOID TUMOR	GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS	LEIOMYOSARCOMA (LMS)	MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)	MYXOFIBROSARCOMA	PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA	SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED	SYNOVIAL SARCOMA - BIPHASIC	SYNOVIAL SARCOMA - MONOPHASIC	UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
ALL	59	2	1	103	9	23	28	2	2	6	21
DEL PEAK 22(11Q24.2) MUTATED	32	0	0	39	6	16	16	0	0	1	13
DEL PEAK 22(11Q24.2) WILD-TYPE	27	2	1	64	3	7	12	2	2	5	8

Figure S132. Get High-res Image Gene #47: 'del_11q24.2' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_11q24.2' versus 'RESIDUAL_TUMOR'

P value = 0.00431 (Fisher's exact test), Q value = 0.038

Table S133. Gene #47: 'del_11q24.2' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	152	68	9	26
DEL PEAK 22(11Q24.2) MUTATED	61	45	4	12
DEL PEAK 22(11Q24.2) WILD-TYPE	91	23	5	14

Figure S133. Get High-res Image Gene #47: 'del_11q24.2' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'del_12p13.1' versus 'GENDER'

P value = 0.0342 (Fisher's exact test), Q value = 0.15

Table S134. Gene #48: 'del_12p13.1' versus Clinical Feature #4: 'GENDER'

nPatients	FEMALE	MALE
ALL	139	117
DEL PEAK 23(12P13.1) MUTATED	39	48
DEL PEAK 23(12P13.1) WILD-TYPE	100	69

Figure S134. Get High-res Image Gene #48: 'del_12p13.1' versus Clinical Feature #4: 'GENDER'

'del_12p13.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.0568 (Fisher's exact test), Q value = 0.21

Table S135. Gene #48: 'del_12p13.1' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	DEDIFFERENTIATED LIPOSARCOMA	DESMOID TUMOR	GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS	LEIOMYOSARCOMA (LMS)	MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)	MYXOFIBROSARCOMA	PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA	SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED	SYNOVIAL SARCOMA - BIPHASIC	SYNOVIAL SARCOMA - MONOPHASIC	UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
ALL	59	2	1	103	9	23	28	2	2	6	21
DEL PEAK 23(12P13.1) MUTATED	20	0	0	33	2	10	17	0	0	0	5
DEL PEAK 23(12P13.1) WILD-TYPE	39	2	1	70	7	13	11	2	2	6	16

Figure S135. Get High-res Image Gene #48: 'del_12p13.1' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_12q12' versus 'Time to Death'

P value = 0.0387 (logrank test), Q value = 0.16

Table S136. Gene #49: 'del_12q12' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	256	94	0.5 - 188.2 (26.4)
DEL PEAK 24(12Q12) MUTATED	56	26	1.1 - 86.1 (26.3)
DEL PEAK 24(12Q12) WILD-TYPE	200	68	0.5 - 188.2 (27.1)

Figure S136. Get High-res Image Gene #49: 'del_12q12' versus Clinical Feature #1: 'Time to Death'

'del_12q12' versus 'RACE'

P value = 0.0365 (Fisher's exact test), Q value = 0.16

Table S137. Gene #49: 'del_12q12' versus Clinical Feature #8: 'RACE'

nPatients	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	6	18	223
DEL PEAK 24(12Q12) MUTATED	0	8	45
DEL PEAK 24(12Q12) WILD-TYPE	6	10	178

Figure S137. Get High-res Image Gene #49: 'del_12q12' versus Clinical Feature #8: 'RACE'

'del_12q24.33' versus 'YEARS_TO_BIRTH'

P value = 0.0037 (Wilcoxon-test), Q value = 0.035

Table S138. Gene #50: 'del_12q24.33' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
DEL PEAK 25(12Q24.33) MUTATED	69	65.3 (12.6)
DEL PEAK 25(12Q24.33) WILD-TYPE	186	59.3 (15.1)

Figure S138. Get High-res Image Gene #50: 'del_12q24.33' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_13q14.2' versus 'YEARS_TO_BIRTH'

P value = 0.00199 (Wilcoxon-test), Q value = 0.024

Table S139. Gene #51: 'del_13q14.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
DEL PEAK 26(13Q14.2) MUTATED	179	62.9 (13.5)
DEL PEAK 26(13Q14.2) WILD-TYPE	76	56.3 (16.3)

Figure S139. Get High-res Image Gene #51: 'del_13q14.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_13q14.2' versus 'TUMOR_TISSUE_SITE'

P value = 0.0109 (Fisher's exact test), Q value = 0.073

Table S140. Gene #51: 'del_13q14.2' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	CHEST - BREAST	CHEST - CHEST WALL	CHEST - LUNG/PLEURA	CHEST - MEDIASTINUM	CHEST - OTHER (PLEASE SPECIFY	GYNECOLOGICAL - OVARY	GYNECOLOGICAL - UTERUS	HEAD AND NECK - HEAD	HEAD AND NECK - NECK	HEAD AND NECK - OTHER (PLEASE SPECIFY	LOWER ABDOMINAL/PELVIC - BLADDER	LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY	LOWER ABDOMINAL/PELVIC - PELVIC	LOWER ABDOMINAL/PELVIC - SPERMATIC CORD	LOWER EXTREMITY - FOOT/ANKLE	LOWER EXTREMITY - GROIN	LOWER EXTREMITY - LOWER LEG/CALF	LOWER EXTREMITY - OTHER (PLEASE SPECIFY	LOWER EXTREMITY - THIGH/KNEE	RETROPERITONEUM/UPPER ABDOMINAL - COLON	RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC	RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL	RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY	RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY	RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS	RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM	RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES	SUPERFICIAL TRUNK - ABDOMINAL WALL	SUPERFICIAL TRUNK - BACK	SUPERFICIAL TRUNK - BUTTOCK	SUPERFICIAL TRUNK - FLANK	UPPER EXTREMITY - SHOULDER/AXILLA	UPPER EXTREMITY - UPPER ARM/ELBOW
ALL	1	7	2	1	2	1	28	2	1	2	1	2	10	2	4	2	17	5	43	4	2	5	8	2	1	73	3	2	5	4	1	7	5
DEL PEAK 26(13Q14.2) MUTATED	1	5	0	1	2	1	25	1	0	1	0	1	5	0	1	1	14	5	34	3	2	1	6	2	1	46	2	2	3	3	0	6	4
DEL PEAK 26(13Q14.2) WILD-TYPE	0	2	2	0	0	0	3	1	1	1	1	1	5	2	3	1	3	0	9	1	0	4	2	0	0	27	1	0	2	1	1	1	1

Figure S140. Get High-res Image Gene #51: 'del_13q14.2' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_13q14.2' versus 'RADIATION_THERAPY'

P value = 0.0202 (Fisher's exact test), Q value = 0.11

Table S141. Gene #51: 'del_13q14.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	180	69
DEL PEAK 26(13Q14.2) MUTATED	118	56
DEL PEAK 26(13Q14.2) WILD-TYPE	62	13

Figure S141. Get High-res Image Gene #51: 'del_13q14.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_13q14.2' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00054

Table S142. Gene #51: 'del_13q14.2' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	DEDIFFERENTIATED LIPOSARCOMA	DESMOID TUMOR	GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS	LEIOMYOSARCOMA (LMS)	MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)	MYXOFIBROSARCOMA	PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA	SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED	SYNOVIAL SARCOMA - BIPHASIC	SYNOVIAL SARCOMA - MONOPHASIC	UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
ALL	59	2	1	103	9	23	28	2	2	6	21
DEL PEAK 26(13Q14.2) MUTATED	26	0	0	88	6	18	24	0	0	1	17
DEL PEAK 26(13Q14.2) WILD-TYPE	33	2	1	15	3	5	4	2	2	5	4

Figure S142. Get High-res Image Gene #51: 'del_13q14.2' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_14q24.1' versus 'TUMOR_TISSUE_SITE'

P value = 0.0339 (Fisher's exact test), Q value = 0.15

Table S143. Gene #52: 'del_14q24.1' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	CHEST - BREAST	CHEST - CHEST WALL	CHEST - LUNG/PLEURA	CHEST - MEDIASTINUM	CHEST - OTHER (PLEASE SPECIFY	GYNECOLOGICAL - OVARY	GYNECOLOGICAL - UTERUS	HEAD AND NECK - HEAD	HEAD AND NECK - NECK	HEAD AND NECK - OTHER (PLEASE SPECIFY	LOWER ABDOMINAL/PELVIC - BLADDER	LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY	LOWER ABDOMINAL/PELVIC - PELVIC	LOWER ABDOMINAL/PELVIC - SPERMATIC CORD	LOWER EXTREMITY - FOOT/ANKLE	LOWER EXTREMITY - GROIN	LOWER EXTREMITY - LOWER LEG/CALF	LOWER EXTREMITY - OTHER (PLEASE SPECIFY	LOWER EXTREMITY - THIGH/KNEE	RETROPERITONEUM/UPPER ABDOMINAL - COLON	RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC	RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL	RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY	RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY	RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS	RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM	RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES	SUPERFICIAL TRUNK - ABDOMINAL WALL	SUPERFICIAL TRUNK - BACK	SUPERFICIAL TRUNK - BUTTOCK	SUPERFICIAL TRUNK - FLANK	UPPER EXTREMITY - SHOULDER/AXILLA	UPPER EXTREMITY - UPPER ARM/ELBOW
ALL	1	7	2	1	2	1	28	2	1	2	1	2	10	2	4	2	17	5	43	4	2	5	8	2	1	73	3	2	5	4	1	7	5
DEL PEAK 27(14Q24.1) MUTATED	0	2	0	0	1	1	21	1	0	0	0	0	3	0	0	0	4	1	12	2	0	0	1	1	0	21	1	0	1	2	0	3	1
DEL PEAK 27(14Q24.1) WILD-TYPE	1	5	2	1	1	0	7	1	1	2	1	2	7	2	4	2	13	4	31	2	2	5	7	1	1	52	2	2	4	2	1	4	4

Figure S143. Get High-res Image Gene #52: 'del_14q24.1' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_16q11.2' versus 'YEARS_TO_BIRTH'

P value = 0.0627 (Wilcoxon-test), Q value = 0.22

Table S144. Gene #53: 'del_16q11.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
DEL PEAK 28(16Q11.2) MUTATED	130	62.6 (13.7)
DEL PEAK 28(16Q11.2) WILD-TYPE	125	59.2 (15.5)

Figure S144. Get High-res Image Gene #53: 'del_16q11.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_16q11.2' versus 'TUMOR_TISSUE_SITE'

P value = 0.047 (Fisher's exact test), Q value = 0.19

Table S145. Gene #53: 'del_16q11.2' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	CHEST - BREAST	CHEST - CHEST WALL	CHEST - LUNG/PLEURA	CHEST - MEDIASTINUM	CHEST - OTHER (PLEASE SPECIFY	GYNECOLOGICAL - OVARY	GYNECOLOGICAL - UTERUS	HEAD AND NECK - HEAD	HEAD AND NECK - NECK	HEAD AND NECK - OTHER (PLEASE SPECIFY	LOWER ABDOMINAL/PELVIC - BLADDER	LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY	LOWER ABDOMINAL/PELVIC - PELVIC	LOWER ABDOMINAL/PELVIC - SPERMATIC CORD	LOWER EXTREMITY - FOOT/ANKLE	LOWER EXTREMITY - GROIN	LOWER EXTREMITY - LOWER LEG/CALF	LOWER EXTREMITY - OTHER (PLEASE SPECIFY	LOWER EXTREMITY - THIGH/KNEE	RETROPERITONEUM/UPPER ABDOMINAL - COLON	RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC	RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL	RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY	RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY	RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS	RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM	RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES	SUPERFICIAL TRUNK - ABDOMINAL WALL	SUPERFICIAL TRUNK - BACK	SUPERFICIAL TRUNK - BUTTOCK	SUPERFICIAL TRUNK - FLANK	UPPER EXTREMITY - SHOULDER/AXILLA	UPPER EXTREMITY - UPPER ARM/ELBOW
ALL	1	7	2	1	2	1	28	2	1	2	1	2	10	2	4	2	17	5	43	4	2	5	8	2	1	73	3	2	5	4	1	7	5
DEL PEAK 28(16Q11.2) MUTATED	1	3	0	1	1	1	18	1	0	0	0	2	6	0	2	1	11	2	29	0	1	1	5	0	0	28	2	1	1	3	1	4	4
DEL PEAK 28(16Q11.2) WILD-TYPE	0	4	2	0	1	0	10	1	1	2	1	0	4	2	2	1	6	3	14	4	1	4	3	2	1	45	1	1	4	1	0	3	1

Figure S145. Get High-res Image Gene #53: 'del_16q11.2' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_16q11.2' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00054

Table S146. Gene #53: 'del_16q11.2' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	DEDIFFERENTIATED LIPOSARCOMA	DESMOID TUMOR	GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS	LEIOMYOSARCOMA (LMS)	MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)	MYXOFIBROSARCOMA	PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA	SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED	SYNOVIAL SARCOMA - BIPHASIC	SYNOVIAL SARCOMA - MONOPHASIC	UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
ALL	59	2	1	103	9	23	28	2	2	6	21
DEL PEAK 28(16Q11.2) MUTATED	13	0	0	66	3	10	20	0	1	0	17
DEL PEAK 28(16Q11.2) WILD-TYPE	46	2	1	37	6	13	8	2	1	6	4

Figure S146. Get High-res Image Gene #53: 'del_16q11.2' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_16q11.2' versus 'RACE'

P value = 0.0129 (Fisher's exact test), Q value = 0.081

Table S147. Gene #53: 'del_16q11.2' versus Clinical Feature #8: 'RACE'

nPatients	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	6	18	223
DEL PEAK 28(16Q11.2) MUTATED	1	14	109
DEL PEAK 28(16Q11.2) WILD-TYPE	5	4	114

Figure S147. Get High-res Image Gene #53: 'del_16q11.2' versus Clinical Feature #8: 'RACE'

'del_16q23.1' versus 'YEARS_TO_BIRTH'

P value = 0.000276 (Wilcoxon-test), Q value = 0.0075

Table S148. Gene #54: 'del_16q23.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
DEL PEAK 29(16Q23.1) MUTATED	133	64.2 (13.6)
DEL PEAK 29(16Q23.1) WILD-TYPE	122	57.4 (15.0)

Figure S148. Get High-res Image Gene #54: 'del_16q23.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_16q23.1' versus 'TUMOR_TISSUE_SITE'

P value = 0.0286 (Fisher's exact test), Q value = 0.14

Table S149. Gene #54: 'del_16q23.1' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	CHEST - BREAST	CHEST - CHEST WALL	CHEST - LUNG/PLEURA	CHEST - MEDIASTINUM	CHEST - OTHER (PLEASE SPECIFY	GYNECOLOGICAL - OVARY	GYNECOLOGICAL - UTERUS	HEAD AND NECK - HEAD	HEAD AND NECK - NECK	HEAD AND NECK - OTHER (PLEASE SPECIFY	LOWER ABDOMINAL/PELVIC - BLADDER	LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY	LOWER ABDOMINAL/PELVIC - PELVIC	LOWER ABDOMINAL/PELVIC - SPERMATIC CORD	LOWER EXTREMITY - FOOT/ANKLE	LOWER EXTREMITY - GROIN	LOWER EXTREMITY - LOWER LEG/CALF	LOWER EXTREMITY - OTHER (PLEASE SPECIFY	LOWER EXTREMITY - THIGH/KNEE	RETROPERITONEUM/UPPER ABDOMINAL - COLON	RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC	RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL	RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY	RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY	RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS	RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM	RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES	SUPERFICIAL TRUNK - ABDOMINAL WALL	SUPERFICIAL TRUNK - BACK	SUPERFICIAL TRUNK - BUTTOCK	SUPERFICIAL TRUNK - FLANK	UPPER EXTREMITY - SHOULDER/AXILLA	UPPER EXTREMITY - UPPER ARM/ELBOW
ALL	1	7	2	1	2	1	28	2	1	2	1	2	10	2	4	2	17	5	43	4	2	5	8	2	1	73	3	2	5	4	1	7	5
DEL PEAK 29(16Q23.1) MUTATED	1	3	0	1	1	1	19	1	0	0	0	2	6	0	2	1	14	3	25	0	1	2	5	0	0	29	2	2	1	3	1	4	4
DEL PEAK 29(16Q23.1) WILD-TYPE	0	4	2	0	1	0	9	1	1	2	1	0	4	2	2	1	3	2	18	4	1	3	3	2	1	44	1	0	4	1	0	3	1

Figure S149. Get High-res Image Gene #54: 'del_16q23.1' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_16q23.1' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00054

Table S150. Gene #54: 'del_16q23.1' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	DEDIFFERENTIATED LIPOSARCOMA	DESMOID TUMOR	GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS	LEIOMYOSARCOMA (LMS)	MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)	MYXOFIBROSARCOMA	PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA	SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED	SYNOVIAL SARCOMA - BIPHASIC	SYNOVIAL SARCOMA - MONOPHASIC	UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
ALL	59	2	1	103	9	23	28	2	2	6	21
DEL PEAK 29(16Q23.1) MUTATED	14	0	0	68	2	13	18	0	1	0	18
DEL PEAK 29(16Q23.1) WILD-TYPE	45	2	1	35	7	10	10	2	1	6	3

Figure S150. Get High-res Image Gene #54: 'del_16q23.1' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_17p13.1' versus 'Time to Death'

P value = 0.0591 (logrank test), Q value = 0.21

Table S151. Gene #55: 'del_17p13.1' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	256	94	0.5 - 188.2 (26.4)
DEL PEAK 30(17P13.1) MUTATED	129	39	0.5 - 188.2 (26.2)
DEL PEAK 30(17P13.1) WILD-TYPE	127	55	0.6 - 130.3 (27.9)

Figure S151. Get High-res Image Gene #55: 'del_17p13.1' versus Clinical Feature #1: 'Time to Death'

'del_17p13.1' versus 'TUMOR_TISSUE_SITE'

P value = 0.0542 (Fisher's exact test), Q value = 0.2

Table S152. Gene #55: 'del_17p13.1' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	CHEST - BREAST	CHEST - CHEST WALL	CHEST - LUNG/PLEURA	CHEST - MEDIASTINUM	CHEST - OTHER (PLEASE SPECIFY	GYNECOLOGICAL - OVARY	GYNECOLOGICAL - UTERUS	HEAD AND NECK - HEAD	HEAD AND NECK - NECK	HEAD AND NECK - OTHER (PLEASE SPECIFY	LOWER ABDOMINAL/PELVIC - BLADDER	LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY	LOWER ABDOMINAL/PELVIC - PELVIC	LOWER ABDOMINAL/PELVIC - SPERMATIC CORD	LOWER EXTREMITY - FOOT/ANKLE	LOWER EXTREMITY - GROIN	LOWER EXTREMITY - LOWER LEG/CALF	LOWER EXTREMITY - OTHER (PLEASE SPECIFY	LOWER EXTREMITY - THIGH/KNEE	RETROPERITONEUM/UPPER ABDOMINAL - COLON	RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC	RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL	RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY	RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY	RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS	RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM	RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES	SUPERFICIAL TRUNK - ABDOMINAL WALL	SUPERFICIAL TRUNK - BACK	SUPERFICIAL TRUNK - BUTTOCK	SUPERFICIAL TRUNK - FLANK	UPPER EXTREMITY - SHOULDER/AXILLA	UPPER EXTREMITY - UPPER ARM/ELBOW
ALL	1	7	2	1	2	1	28	2	1	2	1	2	10	2	4	2	17	5	43	4	2	5	8	2	1	73	3	2	5	4	1	7	5
DEL PEAK 30(17P13.1) MUTATED	0	4	0	1	1	0	16	0	0	0	0	1	3	0	2	0	10	3	27	4	1	1	4	1	1	28	2	2	2	4	1	5	4
DEL PEAK 30(17P13.1) WILD-TYPE	1	3	2	0	1	1	12	2	1	2	1	1	7	2	2	2	7	2	16	0	1	4	4	1	0	45	1	0	3	0	0	2	1

Figure S152. Get High-res Image Gene #55: 'del_17p13.1' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_17p13.1' versus 'GENDER'

P value = 0.0596 (Fisher's exact test), Q value = 0.21

Table S153. Gene #55: 'del_17p13.1' versus Clinical Feature #4: 'GENDER'

nPatients	FEMALE	MALE
ALL	139	117
DEL PEAK 30(17P13.1) MUTATED	78	51
DEL PEAK 30(17P13.1) WILD-TYPE	61	66

Figure S153. Get High-res Image Gene #55: 'del_17p13.1' versus Clinical Feature #4: 'GENDER'

'del_17p13.1' versus 'RADIATION_THERAPY'

P value = 0.0333 (Fisher's exact test), Q value = 0.15

Table S154. Gene #55: 'del_17p13.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	180	69
DEL PEAK 30(17P13.1) MUTATED	81	42
DEL PEAK 30(17P13.1) WILD-TYPE	99	27

Figure S154. Get High-res Image Gene #55: 'del_17p13.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_17p13.1' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00054

Table S155. Gene #55: 'del_17p13.1' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	DEDIFFERENTIATED LIPOSARCOMA	DESMOID TUMOR	GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS	LEIOMYOSARCOMA (LMS)	MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)	MYXOFIBROSARCOMA	PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA	SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED	SYNOVIAL SARCOMA - BIPHASIC	SYNOVIAL SARCOMA - MONOPHASIC	UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
ALL	59	2	1	103	9	23	28	2	2	6	21
DEL PEAK 30(17P13.1) MUTATED	11	0	0	66	7	13	16	0	1	0	15
DEL PEAK 30(17P13.1) WILD-TYPE	48	2	1	37	2	10	12	2	1	6	6

Figure S155. Get High-res Image Gene #55: 'del_17p13.1' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_17q11.2' versus 'YEARS_TO_BIRTH'

P value = 0.00369 (Wilcoxon-test), Q value = 0.035

Table S156. Gene #56: 'del_17q11.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
DEL PEAK 31(17Q11.2) MUTATED	81	64.6 (14.5)
DEL PEAK 31(17Q11.2) WILD-TYPE	174	59.2 (14.5)

Figure S156. Get High-res Image Gene #56: 'del_17q11.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_17q11.2' versus 'TUMOR_TISSUE_SITE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00054

Table S157. Gene #56: 'del_17q11.2' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	CHEST - BREAST	CHEST - CHEST WALL	CHEST - LUNG/PLEURA	CHEST - MEDIASTINUM	CHEST - OTHER (PLEASE SPECIFY	GYNECOLOGICAL - OVARY	GYNECOLOGICAL - UTERUS	HEAD AND NECK - HEAD	HEAD AND NECK - NECK	HEAD AND NECK - OTHER (PLEASE SPECIFY	LOWER ABDOMINAL/PELVIC - BLADDER	LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY	LOWER ABDOMINAL/PELVIC - PELVIC	LOWER ABDOMINAL/PELVIC - SPERMATIC CORD	LOWER EXTREMITY - FOOT/ANKLE	LOWER EXTREMITY - GROIN	LOWER EXTREMITY - LOWER LEG/CALF	LOWER EXTREMITY - OTHER (PLEASE SPECIFY	LOWER EXTREMITY - THIGH/KNEE	RETROPERITONEUM/UPPER ABDOMINAL - COLON	RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC	RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL	RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY	RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY	RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS	RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM	RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES	SUPERFICIAL TRUNK - ABDOMINAL WALL	SUPERFICIAL TRUNK - BACK	SUPERFICIAL TRUNK - BUTTOCK	SUPERFICIAL TRUNK - FLANK	UPPER EXTREMITY - SHOULDER/AXILLA	UPPER EXTREMITY - UPPER ARM/ELBOW
ALL	1	7	2	1	2	1	28	2	1	2	1	2	10	2	4	2	17	5	43	4	2	5	8	2	1	73	3	2	5	4	1	7	5
DEL PEAK 31(17Q11.2) MUTATED	1	6	0	0	0	0	4	0	0	0	0	1	0	0	1	0	7	5	20	1	0	1	2	0	1	18	0	2	1	4	0	4	2
DEL PEAK 31(17Q11.2) WILD-TYPE	0	1	2	1	2	1	24	2	1	2	1	1	10	2	3	2	10	0	23	3	2	4	6	2	0	55	3	0	4	0	1	3	3

Figure S157. Get High-res Image Gene #56: 'del_17q11.2' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_17q11.2' versus 'RADIATION_THERAPY'

P value = 0.0098 (Fisher's exact test), Q value = 0.068

Table S158. Gene #56: 'del_17q11.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	180	69
DEL PEAK 31(17Q11.2) MUTATED	49	31
DEL PEAK 31(17Q11.2) WILD-TYPE	131	38

Figure S158. Get High-res Image Gene #56: 'del_17q11.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_17q11.2' versus 'HISTOLOGICAL_TYPE'

P value = 0.00042 (Fisher's exact test), Q value = 0.0095

Table S159. Gene #56: 'del_17q11.2' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	DEDIFFERENTIATED LIPOSARCOMA	DESMOID TUMOR	GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS	LEIOMYOSARCOMA (LMS)	MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)	MYXOFIBROSARCOMA	PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA	SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED	SYNOVIAL SARCOMA - BIPHASIC	SYNOVIAL SARCOMA - MONOPHASIC	UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
ALL	59	2	1	103	9	23	28	2	2	6	21
DEL PEAK 31(17Q11.2) MUTATED	17	0	0	21	4	13	15	0	0	0	11
DEL PEAK 31(17Q11.2) WILD-TYPE	42	2	1	82	5	10	13	2	2	6	10

Figure S159. Get High-res Image Gene #56: 'del_17q11.2' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_17q25.3' versus 'YEARS_TO_BIRTH'

P value = 0.0133 (Wilcoxon-test), Q value = 0.083

Table S160. Gene #57: 'del_17q25.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
DEL PEAK 32(17Q25.3) MUTATED	66	64.4 (13.0)
DEL PEAK 32(17Q25.3) WILD-TYPE	189	59.7 (15.1)

Figure S160. Get High-res Image Gene #57: 'del_17q25.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_18q23' versus 'Time to Death'

P value = 0.019 (logrank test), Q value = 0.11

Table S161. Gene #58: 'del_18q23' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	256	94	0.5 - 188.2 (26.4)
DEL PEAK 33(18Q23) MUTATED	86	39	0.6 - 188.2 (24.4)
DEL PEAK 33(18Q23) WILD-TYPE	170	55	0.5 - 135.5 (28.6)

Figure S161. Get High-res Image Gene #58: 'del_18q23' versus Clinical Feature #1: 'Time to Death'

'del_18q23' versus 'YEARS_TO_BIRTH'

P value = 0.00313 (Wilcoxon-test), Q value = 0.032

Table S162. Gene #58: 'del_18q23' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
DEL PEAK 33(18Q23) MUTATED	86	64.6 (14.4)
DEL PEAK 33(18Q23) WILD-TYPE	169	59.1 (14.5)

Figure S162. Get High-res Image Gene #58: 'del_18q23' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_18q23' versus 'HISTOLOGICAL_TYPE'

P value = 0.00509 (Fisher's exact test), Q value = 0.044

Table S163. Gene #58: 'del_18q23' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	DEDIFFERENTIATED LIPOSARCOMA	DESMOID TUMOR	GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS	LEIOMYOSARCOMA (LMS)	MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)	MYXOFIBROSARCOMA	PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA	SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED	SYNOVIAL SARCOMA - BIPHASIC	SYNOVIAL SARCOMA - MONOPHASIC	UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
ALL	59	2	1	103	9	23	28	2	2	6	21
DEL PEAK 33(18Q23) MUTATED	16	0	0	28	6	9	15	0	0	0	12
DEL PEAK 33(18Q23) WILD-TYPE	43	2	1	75	3	14	13	2	2	6	9

Figure S163. Get High-res Image Gene #58: 'del_18q23' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_19p13.3' versus 'GENDER'

P value = 0.0118 (Fisher's exact test), Q value = 0.077

Table S164. Gene #59: 'del_19p13.3' versus Clinical Feature #4: 'GENDER'

nPatients	FEMALE	MALE
ALL	139	117
DEL PEAK 34(19P13.3) MUTATED	47	23
DEL PEAK 34(19P13.3) WILD-TYPE	92	94

Figure S164. Get High-res Image Gene #59: 'del_19p13.3' versus Clinical Feature #4: 'GENDER'

'del_19p13.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.00251 (Fisher's exact test), Q value = 0.028

Table S165. Gene #59: 'del_19p13.3' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	DEDIFFERENTIATED LIPOSARCOMA	DESMOID TUMOR	GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS	LEIOMYOSARCOMA (LMS)	MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)	MYXOFIBROSARCOMA	PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA	SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED	SYNOVIAL SARCOMA - BIPHASIC	SYNOVIAL SARCOMA - MONOPHASIC	UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
ALL	59	2	1	103	9	23	28	2	2	6	21
DEL PEAK 34(19P13.3) MUTATED	6	0	0	43	3	6	7	0	0	0	5
DEL PEAK 34(19P13.3) WILD-TYPE	53	2	1	60	6	17	21	2	2	6	16

Figure S165. Get High-res Image Gene #59: 'del_19p13.3' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_19q13.43' versus 'Time to Death'

P value = 0.0589 (logrank test), Q value = 0.21

Table S166. Gene #60: 'del_19q13.43' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	256	94	0.5 - 188.2 (26.4)
DEL PEAK 35(19Q13.43) MUTATED	106	32	1.1 - 188.2 (25.9)
DEL PEAK 35(19Q13.43) WILD-TYPE	150	62	0.5 - 143.4 (26.7)

Figure S166. Get High-res Image Gene #60: 'del_19q13.43' versus Clinical Feature #1: 'Time to Death'

'del_19q13.43' versus 'RADIATION_THERAPY'

P value = 0.00412 (Fisher's exact test), Q value = 0.037

Table S167. Gene #60: 'del_19q13.43' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	180	69
DEL PEAK 35(19Q13.43) MUTATED	65	39
DEL PEAK 35(19Q13.43) WILD-TYPE	115	30

Figure S167. Get High-res Image Gene #60: 'del_19q13.43' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_19q13.43' versus 'HISTOLOGICAL_TYPE'

P value = 0.00071 (Fisher's exact test), Q value = 0.014

Table S168. Gene #60: 'del_19q13.43' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	DEDIFFERENTIATED LIPOSARCOMA	DESMOID TUMOR	GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS	LEIOMYOSARCOMA (LMS)	MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)	MYXOFIBROSARCOMA	PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA	SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED	SYNOVIAL SARCOMA - BIPHASIC	SYNOVIAL SARCOMA - MONOPHASIC	UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
ALL	59	2	1	103	9	23	28	2	2	6	21
DEL PEAK 35(19Q13.43) MUTATED	17	0	0	43	5	8	18	0	0	0	15
DEL PEAK 35(19Q13.43) WILD-TYPE	42	2	1	60	4	15	10	2	2	6	6

Figure S168. Get High-res Image Gene #60: 'del_19q13.43' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_21q11.2' versus 'HISTOLOGICAL_TYPE'

P value = 0.0535 (Fisher's exact test), Q value = 0.2

Table S169. Gene #61: 'del_21q11.2' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	DEDIFFERENTIATED LIPOSARCOMA	DESMOID TUMOR	GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS	LEIOMYOSARCOMA (LMS)	MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)	MYXOFIBROSARCOMA	PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA	SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED	SYNOVIAL SARCOMA - BIPHASIC	SYNOVIAL SARCOMA - MONOPHASIC	UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
ALL	59	2	1	103	9	23	28	2	2	6	21
DEL PEAK 36(21Q11.2) MUTATED	8	0	0	18	5	4	7	0	0	0	9
DEL PEAK 36(21Q11.2) WILD-TYPE	51	2	1	85	4	19	21	2	2	6	12

Figure S169. Get High-res Image Gene #61: 'del_21q11.2' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_21q22.3' versus 'YEARS_TO_BIRTH'

P value = 0.000661 (Wilcoxon-test), Q value = 0.013

Table S170. Gene #62: 'del_21q22.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
DEL PEAK 37(21Q22.3) MUTATED	66	66.3 (11.8)
DEL PEAK 37(21Q22.3) WILD-TYPE	189	59.0 (15.2)

Figure S170. Get High-res Image Gene #62: 'del_21q22.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_21q22.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.0766 (Fisher's exact test), Q value = 0.25

Table S171. Gene #62: 'del_21q22.3' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	DEDIFFERENTIATED LIPOSARCOMA	DESMOID TUMOR	GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS	LEIOMYOSARCOMA (LMS)	MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)	MYXOFIBROSARCOMA	PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA	SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED	SYNOVIAL SARCOMA - BIPHASIC	SYNOVIAL SARCOMA - MONOPHASIC	UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
ALL	59	2	1	103	9	23	28	2	2	6	21
DEL PEAK 37(21Q22.3) MUTATED	16	0	0	20	3	5	14	0	0	0	8
DEL PEAK 37(21Q22.3) WILD-TYPE	43	2	1	83	6	18	14	2	2	6	13

Figure S171. Get High-res Image Gene #62: 'del_21q22.3' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_22q13.32' versus 'TUMOR_TISSUE_SITE'

P value = 0.0722 (Fisher's exact test), Q value = 0.24

Table S172. Gene #63: 'del_22q13.32' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	CHEST - BREAST	CHEST - CHEST WALL	CHEST - LUNG/PLEURA	CHEST - MEDIASTINUM	CHEST - OTHER (PLEASE SPECIFY	GYNECOLOGICAL - OVARY	GYNECOLOGICAL - UTERUS	HEAD AND NECK - HEAD	HEAD AND NECK - NECK	HEAD AND NECK - OTHER (PLEASE SPECIFY	LOWER ABDOMINAL/PELVIC - BLADDER	LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY	LOWER ABDOMINAL/PELVIC - PELVIC	LOWER ABDOMINAL/PELVIC - SPERMATIC CORD	LOWER EXTREMITY - FOOT/ANKLE	LOWER EXTREMITY - GROIN	LOWER EXTREMITY - LOWER LEG/CALF	LOWER EXTREMITY - OTHER (PLEASE SPECIFY	LOWER EXTREMITY - THIGH/KNEE	RETROPERITONEUM/UPPER ABDOMINAL - COLON	RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC	RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL	RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY	RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY	RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS	RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM	RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES	SUPERFICIAL TRUNK - ABDOMINAL WALL	SUPERFICIAL TRUNK - BACK	SUPERFICIAL TRUNK - BUTTOCK	SUPERFICIAL TRUNK - FLANK	UPPER EXTREMITY - SHOULDER/AXILLA	UPPER EXTREMITY - UPPER ARM/ELBOW
ALL	1	7	2	1	2	1	28	2	1	2	1	2	10	2	4	2	17	5	43	4	2	5	8	2	1	73	3	2	5	4	1	7	5
DEL PEAK 38(22Q13.32) MUTATED	0	2	0	0	1	1	17	0	0	0	0	1	3	0	0	0	5	2	19	1	1	0	2	1	0	16	0	2	1	3	0	3	2
DEL PEAK 38(22Q13.32) WILD-TYPE	1	5	2	1	1	0	11	2	1	2	1	1	7	2	4	2	12	3	24	3	1	5	6	1	1	57	3	0	4	1	1	4	3

Figure S172. Get High-res Image Gene #63: 'del_22q13.32' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_xp21.1' versus 'YEARS_TO_BIRTH'

P value = 0.0229 (Wilcoxon-test), Q value = 0.12

Table S173. Gene #64: 'del_xp21.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
DEL PEAK 39(XP21.1) MUTATED	55	57.1 (15.4)
DEL PEAK 39(XP21.1) WILD-TYPE	200	62.0 (14.3)

Figure S173. Get High-res Image Gene #64: 'del_xp21.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_xp21.1' versus 'GENDER'

P value = 0.0679 (Fisher's exact test), Q value = 0.23

Table S174. Gene #64: 'del_xp21.1' versus Clinical Feature #4: 'GENDER'

nPatients	FEMALE	MALE
ALL	139	117
DEL PEAK 39(XP21.1) MUTATED	36	19
DEL PEAK 39(XP21.1) WILD-TYPE	103	98

Figure S174. Get High-res Image Gene #64: 'del_xp21.1' versus Clinical Feature #4: 'GENDER'

'del_xp21.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.0509 (Fisher's exact test), Q value = 0.2

Table S175. Gene #64: 'del_xp21.1' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	DEDIFFERENTIATED LIPOSARCOMA	DESMOID TUMOR	GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS	LEIOMYOSARCOMA (LMS)	MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)	MYXOFIBROSARCOMA	PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA	SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED	SYNOVIAL SARCOMA - BIPHASIC	SYNOVIAL SARCOMA - MONOPHASIC	UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
ALL	59	2	1	103	9	23	28	2	2	6	21
DEL PEAK 39(XP21.1) MUTATED	6	0	0	31	3	6	6	1	0	1	1
DEL PEAK 39(XP21.1) WILD-TYPE	53	2	1	72	6	17	22	1	2	5	20

Figure S175. Get High-res Image Gene #64: 'del_xp21.1' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_xq21.1' versus 'Time to Death'

P value = 0.002 (logrank test), Q value = 0.024

Table S176. Gene #65: 'del_xq21.1' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	256	94	0.5 - 188.2 (26.4)
DEL PEAK 40(XQ21.1) MUTATED	114	30	1.4 - 188.2 (30.9)
DEL PEAK 40(XQ21.1) WILD-TYPE	142	64	0.5 - 135.5 (22.7)

Figure S176. Get High-res Image Gene #65: 'del_xq21.1' versus Clinical Feature #1: 'Time to Death'

'del_xq21.1' versus 'GENDER'

P value = 0.0236 (Fisher's exact test), Q value = 0.12

Table S177. Gene #65: 'del_xq21.1' versus Clinical Feature #4: 'GENDER'

nPatients	FEMALE	MALE
ALL	139	117
DEL PEAK 40(XQ21.1) MUTATED	71	43
DEL PEAK 40(XQ21.1) WILD-TYPE	68	74

Figure S177. Get High-res Image Gene #65: 'del_xq21.1' versus Clinical Feature #4: 'GENDER'

'del_xq21.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.00086 (Fisher's exact test), Q value = 0.015

Table S178. Gene #65: 'del_xq21.1' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	DEDIFFERENTIATED LIPOSARCOMA	DESMOID TUMOR	GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS	LEIOMYOSARCOMA (LMS)	MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)	MYXOFIBROSARCOMA	PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA	SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED	SYNOVIAL SARCOMA - BIPHASIC	SYNOVIAL SARCOMA - MONOPHASIC	UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
ALL	59	2	1	103	9	23	28	2	2	6	21
DEL PEAK 40(XQ21.1) MUTATED	16	0	0	62	4	9	10	0	0	1	12
DEL PEAK 40(XQ21.1) WILD-TYPE	43	2	1	41	5	14	18	2	2	5	9

Figure S178. Get High-res Image Gene #65: 'del_xq21.1' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_xq22.3' versus 'Time to Death'

P value = 0.00171 (logrank test), Q value = 0.022

Table S179. Gene #66: 'del_xq22.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	256	94	0.5 - 188.2 (26.4)
DEL PEAK 41(XQ22.3) MUTATED	123	34	1.1 - 188.2 (33.1)
DEL PEAK 41(XQ22.3) WILD-TYPE	133	60	0.5 - 135.5 (22.6)

Figure S179. Get High-res Image Gene #66: 'del_xq22.3' versus Clinical Feature #1: 'Time to Death'

'del_xq22.3' versus 'TUMOR_TISSUE_SITE'

P value = 0.00906 (Fisher's exact test), Q value = 0.066

Table S180. Gene #66: 'del_xq22.3' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	CHEST - BREAST	CHEST - CHEST WALL	CHEST - LUNG/PLEURA	CHEST - MEDIASTINUM	CHEST - OTHER (PLEASE SPECIFY	GYNECOLOGICAL - OVARY	GYNECOLOGICAL - UTERUS	HEAD AND NECK - HEAD	HEAD AND NECK - NECK	HEAD AND NECK - OTHER (PLEASE SPECIFY	LOWER ABDOMINAL/PELVIC - BLADDER	LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY	LOWER ABDOMINAL/PELVIC - PELVIC	LOWER ABDOMINAL/PELVIC - SPERMATIC CORD	LOWER EXTREMITY - FOOT/ANKLE	LOWER EXTREMITY - GROIN	LOWER EXTREMITY - LOWER LEG/CALF	LOWER EXTREMITY - OTHER (PLEASE SPECIFY	LOWER EXTREMITY - THIGH/KNEE	RETROPERITONEUM/UPPER ABDOMINAL - COLON	RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC	RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL	RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY	RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY	RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS	RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM	RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES	SUPERFICIAL TRUNK - ABDOMINAL WALL	SUPERFICIAL TRUNK - BACK	SUPERFICIAL TRUNK - BUTTOCK	SUPERFICIAL TRUNK - FLANK	UPPER EXTREMITY - SHOULDER/AXILLA	UPPER EXTREMITY - UPPER ARM/ELBOW
ALL	1	7	2	1	2	1	28	2	1	2	1	2	10	2	4	2	17	5	43	4	2	5	8	2	1	73	3	2	5	4	1	7	5
DEL PEAK 41(XQ22.3) MUTATED	1	3	0	1	2	0	18	0	0	0	0	2	5	1	1	0	12	3	20	3	1	0	2	0	1	31	2	0	1	4	0	6	3
DEL PEAK 41(XQ22.3) WILD-TYPE	0	4	2	0	0	1	10	2	1	2	1	0	5	1	3	2	5	2	23	1	1	5	6	2	0	42	1	2	4	0	1	1	2

Figure S180. Get High-res Image Gene #66: 'del_xq22.3' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_xq22.3' versus 'GENDER'

P value = 0.0449 (Fisher's exact test), Q value = 0.18

Table S181. Gene #66: 'del_xq22.3' versus Clinical Feature #4: 'GENDER'

nPatients	FEMALE	MALE
ALL	139	117
DEL PEAK 41(XQ22.3) MUTATED	75	48
DEL PEAK 41(XQ22.3) WILD-TYPE	64	69

Figure S181. Get High-res Image Gene #66: 'del_xq22.3' versus Clinical Feature #4: 'GENDER'

'del_xq22.3' versus 'HISTOLOGICAL_TYPE'

P value = 7e-05 (Fisher's exact test), Q value = 0.0023

Table S182. Gene #66: 'del_xq22.3' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	DEDIFFERENTIATED LIPOSARCOMA	DESMOID TUMOR	GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS	LEIOMYOSARCOMA (LMS)	MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)	MYXOFIBROSARCOMA	PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA	SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED	SYNOVIAL SARCOMA - BIPHASIC	SYNOVIAL SARCOMA - MONOPHASIC	UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
ALL	59	2	1	103	9	23	28	2	2	6	21
DEL PEAK 41(XQ22.3) MUTATED	15	0	0	66	4	9	15	0	0	1	13
DEL PEAK 41(XQ22.3) WILD-TYPE	44	2	1	37	5	14	13	2	2	5	8

Figure S182. Get High-res Image Gene #66: 'del_xq22.3' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_xq22.3' versus 'RESIDUAL_TUMOR'

P value = 0.0622 (Fisher's exact test), Q value = 0.22

Table S183. Gene #66: 'del_xq22.3' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	152	68	9	26
DEL PEAK 41(XQ22.3) MUTATED	81	31	3	7
DEL PEAK 41(XQ22.3) WILD-TYPE	71	37	6	19

Figure S183. Get High-res Image Gene #66: 'del_xq22.3' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

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/SARC-TP/19782155/transformed.cor.cli.txt
Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/SARC-TP/19775498/SARC-TP.merged_data.txt
Number of patients = 256
Number of significantly focal cnvs = 66
Number of selected clinical features = 9
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.

Download Results

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

References

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

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

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

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