Correlation between copy number variation genes (focal events) and selected clinical features
Sarcoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C11G0KQN
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlation between copy number variation genes (focal events) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C11G0KQN
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 69 focal events and 9 clinical features across 257 patients, 181 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',  'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.

  • amp_1q24.3 cnv correlated to 'Time to Death' and '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 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE', and 'HISTOLOGICAL_TYPE'.

  • amp_6p21.1 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH', and 'RADIATION_THERAPY'.

  • amp_6q25.1 cnv correlated to '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',  'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.

  • amp_8q24.21 cnv correlated to 'Time to Death'.

  • amp_11q22.2 cnv correlated to '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', 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_19q12 cnv correlated to 'YEARS_TO_BIRTH',  'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.

  • amp_20q13.33 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'GENDER',  'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.

  • amp_21q21.1 cnv correlated to 'YEARS_TO_BIRTH'.

  • 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', 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 'Time to Death',  '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',  'RADIATION_THERAPY', 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_11q23.1 cnv correlated to 'RADIATION_THERAPY' and 'HISTOLOGICAL_TYPE'.

  • del_11q25 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_15q11.2 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH', and 'RACE'.

  • 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 '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 'RADIATION_THERAPY' and 'HISTOLOGICAL_TYPE'.

  • del_21q11.2 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • del_21q22.3 cnv correlated to 'YEARS_TO_BIRTH'.

  • del_22q13.32 cnv correlated to 'GENDER'.

  • 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 69 focal events and 9 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 181 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%) 163 0.0594
(0.219) 		0.00574
(0.0475) 		2e-05
(0.00103) 		0.000429
(0.00987) 		0.667
(0.828) 		1e-05
(0.000621) 		0.00116
(0.0172) 		0.00682
(0.0548) 		1
(1.00)
amp 1p32 1 94 (37%) 163 6.66e-05
(0.00259) 		0.000341
(0.00882) 		0.0273
(0.135) 		0.242
(0.503) 		0.0139
(0.09) 		0.00158
(0.0213) 		0.426
(0.662) 		0.136
(0.344) 		0.159
(0.379)
amp 17q24 3 79 (31%) 178 0.275
(0.539) 		0.0336
(0.152) 		0.227
(0.484) 		0.0299
(0.144) 		0.0244
(0.125) 		0.0139
(0.09) 		0.0375
(0.164) 		0.549
(0.766) 		1
(1.00)
amp 20q13 33 98 (38%) 159 0.0219
(0.118) 		0.000219
(0.00646) 		0.0831
(0.267) 		0.0142
(0.0902) 		0.00948
(0.0684) 		0.0012
(0.0173) 		0.114
(0.315) 		1
(1.00) 		1
(1.00)
del 2q37 3 108 (42%) 149 0.00698
(0.0548) 		0.00718
(0.0557) 		0.0282
(0.138) 		0.9
(0.974) 		0.0159
(0.0934) 		0.00162
(0.0214) 		0.781
(0.905) 		0.444
(0.681) 		0.396
(0.643)
del xq22 3 123 (48%) 134 0.00565
(0.0474) 		0.782
(0.905) 		0.00859
(0.0643) 		0.0448
(0.184) 		0.268
(0.529) 		3e-05
(0.00133) 		0.0596
(0.219) 		0.654
(0.828) 		0.372
(0.622)
amp 3p12 1 69 (27%) 188 0.115
(0.317) 		9.19e-06
(0.000621) 		0.00049
(0.0109) 		0.397
(0.643) 		0.0588
(0.219) 		3e-05
(0.00133) 		0.489
(0.722) 		0.73
(0.87) 		0.326
(0.572)
amp 4q12 78 (30%) 179 0.319
(0.572) 		0.0328
(0.151) 		0.0266
(0.132) 		0.587
(0.801) 		0.00983
(0.0701) 		8e-05
(0.00276) 		0.522
(0.748) 		0.555
(0.77) 		1
(1.00)
amp 5p15 33 119 (46%) 138 0.0402
(0.172) 		0.00112
(0.0172) 		0.0447
(0.184) 		0.21
(0.454) 		0.0929
(0.282) 		0.0168
(0.0956) 		0.604
(0.813) 		0.941
(1.00) 		1
(1.00)
amp 8p11 22 81 (32%) 176 0.00331
(0.032) 		0.000986
(0.0161) 		0.662
(0.828) 		1
(1.00) 		0.0711
(0.245) 		0.0726
(0.249) 		0.661
(0.828) 		0.0885
(0.276) 		0.66
(0.828)
amp 17p11 2 104 (40%) 153 0.155
(0.375) 		0.015
(0.0934) 		0.0445
(0.184) 		0.252
(0.512) 		0.000373
(0.00919) 		2e-05
(0.00103) 		0.231
(0.487) 		0.496
(0.727) 		1
(1.00)
del 1p36 32 69 (27%) 188 0.058
(0.219) 		0.145
(0.359) 		0.0855
(0.27) 		0.000385
(0.00919) 		0.0112
(0.0774) 		1e-05
(0.000621) 		0.102
(0.297) 		0.67
(0.828) 		0.328
(0.572)
del 2p25 3 94 (37%) 163 0.376
(0.622) 		0.0551
(0.21) 		0.312
(0.572) 		0.0195
(0.107) 		0.248
(0.508) 		0.00191
(0.0237) 		0.0756
(0.251) 		0.00241
(0.0266) 		0.159
(0.379)
del 2q37 3 110 (43%) 147 0.0369
(0.163) 		0.00219
(0.0248) 		0.00692
(0.0548) 		0.53
(0.754) 		0.0905
(0.28) 		0.00552
(0.0474) 		0.601
(0.812) 		0.537
(0.758) 		1
(1.00)
del 10q23 31 138 (54%) 119 0.101
(0.297) 		0.0157
(0.0934) 		0.534
(0.757) 		0.21
(0.454) 		0.0707
(0.245) 		1e-05
(0.000621) 		0.846
(0.955) 		0.0158
(0.0934) 		0.179
(0.407)
del 11q25 123 (48%) 134 0.48
(0.715) 		0.00606
(0.0495) 		0.109
(0.309) 		0.709
(0.853) 		0.00775
(0.0594) 		0.0017
(0.0215) 		0.0262
(0.132) 		0.652
(0.828) 		0.371
(0.622)
del 13q14 2 180 (70%) 77 0.542
(0.76) 		0.00129
(0.0182) 		0.0142
(0.0902) 		0.0767
(0.253) 		0.0223
(0.119) 		1e-05
(0.000621) 		0.691
(0.841) 		0.557
(0.77) 		0.152
(0.37)
del 16q11 2 130 (51%) 127 0.731
(0.87) 		0.0509
(0.2) 		0.0593
(0.219) 		0.105
(0.3) 		0.125
(0.329) 		1e-05
(0.000621) 		0.327
(0.572) 		0.0126
(0.0841) 		1
(1.00)
del 17p13 1 129 (50%) 128 0.0911
(0.28) 		0.176
(0.402) 		0.0635
(0.228) 		0.0455
(0.185) 		0.0503
(0.199) 		1e-05
(0.000621) 		0.514
(0.744) 		0.109
(0.309) 		0.683
(0.836)
del 17q11 2 81 (32%) 176 0.256
(0.515) 		0.00312
(0.0312) 		8e-05
(0.00276) 		0.346
(0.592) 		0.0105
(0.0742) 		0.0006
(0.0119) 		0.652
(0.828) 		0.648
(0.828) 		1
(1.00)
amp 1q21 3 105 (41%) 152 0.203
(0.444) 		0.0165
(0.0956) 		0.103
(0.299) 		0.0752
(0.251) 		0.0466
(0.187) 		0.00826
(0.0626) 		0.351
(0.598) 		0.938
(1.00) 		0.651
(0.828)
amp 6p21 1 60 (23%) 197 0.0031
(0.0312) 		0.0613
(0.224) 		0.67
(0.828) 		0.375
(0.622) 		0.0316
(0.148) 		0.172
(0.398) 		0.331
(0.572) 		0.122
(0.328) 		0.336
(0.577)
amp 7q31 2 77 (30%) 180 0.112
(0.311) 		1.05e-06
(0.000621) 		0.093
(0.282) 		0.892
(0.974) 		0.0153
(0.0934) 		0.00297
(0.0307) 		0.964
(1.00) 		1
(1.00) 		0.648
(0.828)
amp 13q34 54 (21%) 203 0.13
(0.337) 		0.197
(0.432) 		0.0537
(0.206) 		0.0911
(0.28) 		0.0406
(0.173) 		0.086
(0.27) 		0.54
(0.758) 		0.0346
(0.156) 		0.588
(0.801)
amp 17p12 102 (40%) 155 0.122
(0.328) 		0.0137
(0.09) 		0.481
(0.715) 		0.702
(0.852) 		0.0459
(0.185) 		0.00385
(0.0352) 		0.671
(0.828) 		0.774
(0.904) 		0.4
(0.644)
amp 19q12 93 (36%) 164 0.0738
(0.251) 		0.000522
(0.0112) 		0.279
(0.542) 		0.298
(0.559) 		0.0588
(0.219) 		0.0167
(0.0956) 		0.473
(0.705) 		0.873
(0.97) 		0.654
(0.828)
amp xp21 2 97 (38%) 160 0.96
(1.00) 		0.0291
(0.141) 		0.296
(0.558) 		0.522
(0.748) 		0.0212
(0.116) 		0.00892
(0.0659) 		0.465
(0.697) 		0.822
(0.935) 		0.651
(0.828)
del 1q44 80 (31%) 177 0.164
(0.385) 		0.00196
(0.0238) 		0.684
(0.836) 		0.787
(0.907) 		0.000919
(0.0159) 		6e-05
(0.00248) 		0.138
(0.344) 		0.228
(0.484) 		1
(1.00)
del 4q35 1 94 (37%) 163 0.136
(0.344) 		0.00166
(0.0215) 		0.265
(0.525) 		0.605
(0.813) 		0.00358
(0.0332) 		0.0115
(0.0775) 		0.23
(0.487) 		0.289
(0.553) 		0.161
(0.379)
del 8p23 3 81 (32%) 176 0.0689
(0.242) 		0.0421
(0.178) 		0.653
(0.828) 		0.501
(0.731) 		0.0524
(0.205) 		0.128
(0.332) 		0.213
(0.457) 		0.597
(0.81) 		1
(1.00)
del 9p21 3 114 (44%) 143 0.0185
(0.103) 		0.0015
(0.0207) 		0.706
(0.852) 		0.615
(0.822) 		0.329
(0.572) 		0.0303
(0.145) 		0.295
(0.558) 		0.505
(0.734) 		1
(1.00)
del 9q34 3 61 (24%) 196 0.111
(0.311) 		0.255
(0.515) 		0.186
(0.418) 		0.462
(0.695) 		0.147
(0.361) 		0.00063
(0.0119) 		0.00296
(0.0307) 		0.0182
(0.102) 		1
(1.00)
del 10p15 3 128 (50%) 129 0.898
(0.974) 		0.0229
(0.121) 		0.426
(0.662) 		0.104
(0.3) 		0.0695
(0.242) 		0.00012
(0.00392) 		0.294
(0.558) 		0.194
(0.431) 		0.212
(0.457)
del 10q26 3 132 (51%) 125 0.395
(0.642) 		0.00219
(0.0248) 		0.17
(0.396) 		0.383
(0.629) 		0.328
(0.572) 		1e-05
(0.000621) 		1
(1.00) 		0.0649
(0.232) 		0.194
(0.431)
del 15q11 2 47 (18%) 210 0.00909
(0.0664) 		0.000325
(0.00878) 		0.0835
(0.267) 		0.423
(0.662) 		0.206
(0.45) 		0.264
(0.525) 		0.244
(0.503) 		0.0451
(0.184) 		0.588
(0.801)
del 16q23 1 134 (52%) 123 0.14
(0.348) 		0.000198
(0.00615) 		0.0307
(0.146) 		0.106
(0.302) 		0.402
(0.644) 		1e-05
(0.000621) 		0.121
(0.328) 		0.136
(0.344) 		0.666
(0.828)
del 18q23 86 (33%) 171 0.00342
(0.0321) 		0.00262
(0.028) 		0.759
(0.893) 		0.426
(0.662) 		0.106
(0.303) 		0.0046
(0.0414) 		0.408
(0.65) 		1
(1.00) 		0.665
(0.828)
del xp21 1 55 (21%) 202 0.673
(0.829) 		0.0265
(0.132) 		0.176
(0.402) 		0.0672
(0.238) 		0.615
(0.822) 		0.0537
(0.206) 		0.29
(0.553) 		0.415
(0.657) 		0.244
(0.503)
del xq21 1 114 (44%) 143 0.00318
(0.0313) 		0.245
(0.503) 		0.417
(0.657) 		0.0233
(0.121) 		0.888
(0.974) 		0.00062
(0.0119) 		0.261
(0.523) 		0.285
(0.547) 		0.38
(0.628)
amp 1q24 3 102 (40%) 155 0.0439
(0.184) 		0.122
(0.328) 		0.381
(0.628) 		0.898
(0.974) 		0.0332
(0.152) 		0.311
(0.572) 		0.632
(0.828) 		0.638
(0.828) 		1
(1.00)
del 3p21 31 65 (25%) 192 0.452
(0.688) 		0.316
(0.572) 		0.0862
(0.27) 		0.886
(0.974) 		0.0382
(0.165) 		0.00097
(0.0161) 		0.423
(0.662) 		0.555
(0.77) 		1
(1.00)
del 3q13 31 51 (20%) 206 0.126
(0.329) 		0.0112
(0.0774) 		0.635
(0.828) 		0.436
(0.672) 		0.0238
(0.123) 		0.116
(0.318) 		0.0952
(0.285) 		0.817
(0.931) 		1
(1.00)
del 6q14 1 78 (30%) 179 0.647
(0.828) 		0.235
(0.492) 		0.0254
(0.129) 		0.892
(0.974) 		0.0153
(0.0934) 		0.097
(0.287) 		0.896
(0.974) 		0.806
(0.921) 		1
(1.00)
del 11p15 5 110 (43%) 147 0.196
(0.431) 		0.00335
(0.032) 		0.466
(0.697) 		0.53
(0.754) 		0.0676
(0.239) 		0.173
(0.398) 		0.678
(0.833) 		0.642
(0.828) 		0.385
(0.631)
del 11q23 1 118 (46%) 139 0.416
(0.657) 		0.124
(0.329) 		0.0967
(0.287) 		0.9
(0.974) 		0.0021
(0.0246) 		0.0225
(0.119) 		0.304
(0.569) 		0.736
(0.874) 		0.375
(0.622)
del 12p13 1 87 (34%) 170 0.624
(0.828) 		0.138
(0.344) 		0.761
(0.894) 		0.0353
(0.158) 		0.883
(0.974) 		0.0635
(0.228) 		0.836
(0.946) 		0.713
(0.856) 		0.663
(0.828)
del 12q12 56 (22%) 201 0.0181
(0.102) 		0.127
(0.332) 		0.813
(0.928) 		0.651
(0.828) 		0.402
(0.644) 		0.402
(0.644) 		0.853
(0.96) 		0.0357
(0.158) 		0.589
(0.801)
del 19p13 3 70 (27%) 187 0.772
(0.904) 		0.523
(0.749) 		0.238
(0.498) 		0.0115
(0.0775) 		0.758
(0.893) 		0.00244
(0.0266) 		0.828
(0.938) 		0.727
(0.868) 		0.328
(0.572)
del 19q13 43 106 (41%) 151 0.116
(0.318) 		0.317
(0.572) 		0.306
(0.57) 		0.254
(0.514) 		0.0159
(0.0934) 		0.00069
(0.0126) 		0.146
(0.359) 		0.313
(0.572) 		0.39
(0.638)
amp 2p11 2 64 (25%) 193 0.489
(0.722) 		0.000745
(0.0132) 		0.955
(1.00) 		0.148
(0.361) 		0.518
(0.748) 		0.458
(0.692) 		0.706
(0.852) 		0.131
(0.338) 		1
(1.00)
amp 6q25 1 75 (29%) 182 0.778
(0.905) 		0.0774
(0.254) 		0.492
(0.722) 		0.0752
(0.251) 		0.0924
(0.282) 		0.00028
(0.0079) 		0.284
(0.547) 		0.867
(0.967) 		0.632
(0.828)
amp 8q24 21 83 (32%) 174 0.00106
(0.0169) 		0.354
(0.6) 		0.414
(0.657) 		0.894
(0.974) 		0.658
(0.828) 		0.0989
(0.291) 		0.188
(0.42) 		0.158
(0.379) 		0.334
(0.575)
amp 11q22 2 36 (14%) 221 0.0779
(0.255) 		0.00564
(0.0474) 		0.896
(0.974) 		0.719
(0.862) 		0.321
(0.572) 		0.0951
(0.285) 		0.783
(0.905) 		0.16
(0.379) 		0.539
(0.758)
amp 15q26 3 84 (33%) 173 0.453
(0.688) 		0.0157
(0.0934) 		0.511
(0.741) 		0.233
(0.49) 		0.375
(0.622) 		0.193
(0.431) 		0.571
(0.786) 		0.618
(0.823) 		0.347
(0.592)
amp 21q21 1 73 (28%) 184 0.135
(0.344) 		0.00471
(0.0418) 		0.5
(0.73) 		0.0955
(0.285) 		0.28
(0.542) 		0.157
(0.379) 		0.489
(0.722) 		0.582
(0.798) 		0.325
(0.572)
amp xq21 1 46 (18%) 211 0.125
(0.329) 		0.0497
(0.198) 		0.998
(1.00) 		0.331
(0.572) 		0.27
(0.531) 		0.331
(0.572) 		0.865
(0.967) 		0.244
(0.503) 		0.226
(0.483)
del 5p15 33 33 (13%) 224 0.266
(0.525) 		0.927
(0.999) 		0.0383
(0.165) 		1
(1.00) 		0.539
(0.758) 		0.803
(0.92) 		0.954
(1.00) 		0.878
(0.974) 		1
(1.00)
del 6p25 3 81 (32%) 176 0.25
(0.508) 		0.785
(0.906) 		0.367
(0.62) 		0.788
(0.907) 		1
(1.00) 		0.0325
(0.151) 		0.972
(1.00) 		0.703
(0.852) 		0.327
(0.572)
del 9p24 3 100 (39%) 157 0.195
(0.431) 		0.00116
(0.0172) 		0.37
(0.622) 		0.521
(0.748) 		0.668
(0.828) 		0.825
(0.936) 		0.61
(0.818) 		1
(1.00) 		0.653
(0.828)
del 12q24 33 70 (27%) 187 0.683
(0.836) 		0.002
(0.0238) 		0.407
(0.65) 		0.122
(0.328) 		0.754
(0.89) 		0.43
(0.666) 		0.45
(0.686) 		0.393
(0.641) 		0.326
(0.572)
del 14q24 1 80 (31%) 177 0.629
(0.828) 		0.988
(1.00) 		0.0319
(0.149) 		0.138
(0.344) 		0.449
(0.686) 		0.802
(0.92) 		0.0851
(0.27) 		0.649
(0.828) 		0.326
(0.572)
del 17q25 3 67 (26%) 190 0.159
(0.379) 		0.00547
(0.0474) 		0.926
(0.999) 		1
(1.00) 		0.632
(0.828) 		0.457
(0.691) 		0.667
(0.828) 		0.721
(0.862) 		0.328
(0.572)
del 21q11 2 51 (20%) 206 0.849
(0.957) 		0.163
(0.383) 		0.873
(0.97) 		0.531
(0.754) 		0.298
(0.559) 		0.0534
(0.206) 		0.601
(0.812) 		0.687
(0.838) 		0.262
(0.523)
del 21q22 3 66 (26%) 191 0.75
(0.889) 		0.000554
(0.0115) 		0.859
(0.963) 		0.887
(0.974) 		0.111
(0.311) 		0.0748
(0.251) 		0.549
(0.766) 		0.929
(1) 		1
(1.00)
del 22q13 32 83 (32%) 174 0.431
(0.666) 		0.169
(0.395) 		0.0798
(0.259) 		0.062
(0.225) 		0.655
(0.828) 		0.289
(0.553) 		0.868
(0.967) 		1
(1.00) 		1
(1.00)
amp 19p13 2 108 (42%) 149 0.961
(1.00) 		0.28
(0.542) 		0.081
(0.262) 		0.311
(0.572) 		0.888
(0.974) 		0.0754
(0.251) 		0.63
(0.828) 		0.774
(0.904) 		0.655
(0.828)
del 3q29 54 (21%) 203 0.856
(0.961) 		0.49
(0.722) 		0.568
(0.783) 		0.358
(0.607) 		0.124
(0.329) 		0.25
(0.508) 		0.462
(0.695) 		0.321
(0.572) 		1
(1.00)
del 7q36 3 71 (28%) 186 0.184
(0.415) 		0.437
(0.672) 		0.326
(0.572) 		0.78
(0.905) 		0.276
(0.539) 		0.182
(0.413) 		0.133
(0.341) 		0.426
(0.662) 		1
(1.00)
del 18p11 32 68 (26%) 189 0.176
(0.402) 		0.324
(0.572) 		0.971
(1.00) 		0.572
(0.786) 		0.754
(0.89) 		0.704
(0.852) 		0.556
(0.77) 		0.327
(0.572) 		0.327
(0.572)
'amp_1p32.1' versus 'Time to Death'

P value = 6.66e-05 (logrank test), Q value = 0.0026

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

nPatients nDeath Duration Range (Median), Month
ALL 257 98 0.5 - 188.2 (31.1)
AMP PEAK 1(1P32.1) MUTATED 94 48 0.6 - 106.5 (24.8)
AMP PEAK 1(1P32.1) WILD-TYPE 163 50 0.5 - 188.2 (34.7)

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 = 0.000341 (Wilcoxon-test), Q value = 0.0088

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

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
AMP PEAK 1(1P32.1) MUTATED 94 65.3 (13.0)
AMP PEAK 1(1P32.1) WILD-TYPE 162 58.2 (15.1)

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 = 0.0273 (Fisher's exact test), Q value = 0.13

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 44 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 17 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 = 0.0139 (Fisher's exact test), Q value = 0.09

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

nPatients NO YES
ALL 179 72
AMP PEAK 1(1P32.1) MUTATED 58 36
AMP PEAK 1(1P32.1) WILD-TYPE 121 36

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 = 0.00158 (Fisher's exact test), Q value = 0.021

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 24 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 12 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 = 0.0165 (Wilcoxon-test), Q value = 0.096

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

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
AMP PEAK 2(1Q21.3) MUTATED 104 63.3 (12.8)
AMP PEAK 2(1Q21.3) WILD-TYPE 152 59.2 (15.7)

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

'amp_1q21.3' versus 'RADIATION_THERAPY'

P value = 0.0466 (Fisher's exact test), Q value = 0.19

Table S7.  Gene #2: 'amp_1q21.3' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 179 72
AMP PEAK 2(1Q21.3) MUTATED 66 37
AMP PEAK 2(1Q21.3) WILD-TYPE 113 35

Figure S7.  Get High-res Image Gene #2: 'amp_1q21.3' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_1q21.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.00826 (Fisher's exact test), Q value = 0.063

Table S8.  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 24 28 2 2 6 21
AMP PEAK 2(1Q21.3) MUTATED 16 0 0 45 3 10 18 1 0 0 12
AMP PEAK 2(1Q21.3) WILD-TYPE 43 2 1 58 6 14 10 1 2 6 9

Figure S8.  Get High-res Image Gene #2: 'amp_1q21.3' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'amp_1q24.3' versus 'Time to Death'

P value = 0.0439 (logrank test), Q value = 0.18

Table S9.  Gene #3: 'amp_1q24.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 257 98 0.5 - 188.2 (31.1)
AMP PEAK 3(1Q24.3) MUTATED 102 46 0.6 - 171.1 (31.2)
AMP PEAK 3(1Q24.3) WILD-TYPE 155 52 0.5 - 188.2 (31.1)

Figure S9.  Get High-res Image Gene #3: 'amp_1q24.3' versus Clinical Feature #1: 'Time to Death'

'amp_1q24.3' versus 'RADIATION_THERAPY'

P value = 0.0332 (Fisher's exact test), Q value = 0.15

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

nPatients NO YES
ALL 179 72
AMP PEAK 3(1Q24.3) MUTATED 65 37
AMP PEAK 3(1Q24.3) WILD-TYPE 114 35

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 = 0.000745 (Wilcoxon-test), Q value = 0.013

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

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
AMP PEAK 4(2P11.2) MUTATED 64 66.4 (12.5)
AMP PEAK 4(2P11.2) WILD-TYPE 192 59.0 (15.0)

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 = 9.19e-06 (Wilcoxon-test), Q value = 0.00062

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

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
AMP PEAK 5(3P12.1) MUTATED 68 67.6 (13.7)
AMP PEAK 5(3P12.1) WILD-TYPE 188 58.4 (14.4)

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 = 0.00049 (Fisher's exact test), Q value = 0.011

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 44 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 20 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 = 0.0588 (Fisher's exact test), Q value = 0.22

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

nPatients NO YES
ALL 179 72
AMP PEAK 5(3P12.1) MUTATED 42 26
AMP PEAK 5(3P12.1) WILD-TYPE 137 46

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 = 3e-05 (Fisher's exact test), Q value = 0.0013

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 24 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 15 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 = 0.0328 (Wilcoxon-test), Q value = 0.15

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

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
AMP PEAK 6(4Q12) MUTATED 77 64.1 (12.3)
AMP PEAK 6(4Q12) WILD-TYPE 179 59.4 (15.5)

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 = 0.0266 (Fisher's exact test), Q value = 0.13

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 44 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 24 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 = 0.00983 (Fisher's exact test), Q value = 0.07

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

nPatients NO YES
ALL 179 72
AMP PEAK 6(4Q12) MUTATED 46 31
AMP PEAK 6(4Q12) WILD-TYPE 133 41

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

'amp_4q12' versus 'HISTOLOGICAL_TYPE'

P value = 8e-05 (Fisher's exact test), Q value = 0.0028

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 24 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 12 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 'Time to Death'

P value = 0.0402 (logrank test), Q value = 0.17

Table S20.  Gene #7: 'amp_5p15.33' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 257 98 0.5 - 188.2 (31.1)
AMP PEAK 7(5P15.33) MUTATED 119 52 0.6 - 188.2 (27.3)
AMP PEAK 7(5P15.33) WILD-TYPE 138 46 0.5 - 171.1 (35.1)

Figure S20.  Get High-res Image Gene #7: 'amp_5p15.33' versus Clinical Feature #1: 'Time to Death'

'amp_5p15.33' versus 'YEARS_TO_BIRTH'

P value = 0.00112 (Wilcoxon-test), Q value = 0.017

Table S21.  Gene #7: 'amp_5p15.33' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
AMP PEAK 7(5P15.33) MUTATED 118 64.1 (13.3)
AMP PEAK 7(5P15.33) WILD-TYPE 138 58.0 (15.4)

Figure S21.  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 = 0.0447 (Fisher's exact test), Q value = 0.18

Table S22.  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 44 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 22 4 1 3 6 0 0 35 3 0 3 2 1 0 2

Figure S22.  Get High-res Image Gene #7: 'amp_5p15.33' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'amp_5p15.33' versus 'HISTOLOGICAL_TYPE'

P value = 0.0168 (Fisher's exact test), Q value = 0.096

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 24 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 13 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 = 0.0031 (logrank test), Q value = 0.031

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

nPatients nDeath Duration Range (Median), Month
ALL 257 98 0.5 - 188.2 (31.1)
AMP PEAK 8(6P21.1) MUTATED 60 32 0.6 - 171.1 (27.2)
AMP PEAK 8(6P21.1) WILD-TYPE 197 66 0.5 - 188.2 (32.1)

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 = 0.0613 (Wilcoxon-test), Q value = 0.22

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

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
AMP PEAK 8(6P21.1) MUTATED 59 63.8 (13.2)
AMP PEAK 8(6P21.1) WILD-TYPE 197 60.0 (15.1)

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 = 0.0316 (Fisher's exact test), Q value = 0.15

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

nPatients NO YES
ALL 179 72
AMP PEAK 8(6P21.1) MUTATED 35 24
AMP PEAK 8(6P21.1) WILD-TYPE 144 48

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

'amp_6q25.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.00028 (Fisher's exact test), Q value = 0.0079

Table S27.  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 24 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 12 13 2 2 6 16

Figure S27.  Get High-res Image Gene #9: 'amp_6q25.1' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'amp_7q31.2' versus 'YEARS_TO_BIRTH'

P value = 1.05e-06 (Wilcoxon-test), Q value = 0.00062

Table S28.  Gene #10: 'amp_7q31.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
AMP PEAK 10(7Q31.2) MUTATED 77 67.3 (11.9)
AMP PEAK 10(7Q31.2) WILD-TYPE 179 58.1 (15.0)

Figure S28.  Get High-res Image Gene #10: 'amp_7q31.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_7q31.2' versus 'RADIATION_THERAPY'

P value = 0.0153 (Fisher's exact test), Q value = 0.093

Table S29.  Gene #10: 'amp_7q31.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 179 72
AMP PEAK 10(7Q31.2) MUTATED 46 30
AMP PEAK 10(7Q31.2) WILD-TYPE 133 42

Figure S29.  Get High-res Image Gene #10: 'amp_7q31.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_7q31.2' versus 'HISTOLOGICAL_TYPE'

P value = 0.00297 (Fisher's exact test), Q value = 0.031

Table S30.  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 24 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 14 14 2 2 6 9

Figure S30.  Get High-res Image Gene #10: 'amp_7q31.2' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'amp_8p11.22' versus 'Time to Death'

P value = 0.00331 (logrank test), Q value = 0.032

Table S31.  Gene #11: 'amp_8p11.22' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 257 98 0.5 - 188.2 (31.1)
AMP PEAK 11(8P11.22) MUTATED 81 40 0.6 - 112.0 (22.9)
AMP PEAK 11(8P11.22) WILD-TYPE 176 58 0.5 - 188.2 (34.0)

Figure S31.  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 = 0.000986 (Wilcoxon-test), Q value = 0.016

Table S32.  Gene #11: 'amp_8p11.22' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
AMP PEAK 11(8P11.22) MUTATED 80 65.6 (12.2)
AMP PEAK 11(8P11.22) WILD-TYPE 176 58.6 (15.3)

Figure S32.  Get High-res Image Gene #11: 'amp_8p11.22' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_8p11.22' versus 'RADIATION_THERAPY'

P value = 0.0711 (Fisher's exact test), Q value = 0.25

Table S33.  Gene #11: 'amp_8p11.22' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 179 72
AMP PEAK 11(8P11.22) MUTATED 50 29
AMP PEAK 11(8P11.22) WILD-TYPE 129 43

Figure S33.  Get High-res Image Gene #11: 'amp_8p11.22' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_8p11.22' versus 'HISTOLOGICAL_TYPE'

P value = 0.0726 (Fisher's exact test), Q value = 0.25

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 24 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 12 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 = 0.00106 (logrank test), Q value = 0.017

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

nPatients nDeath Duration Range (Median), Month
ALL 257 98 0.5 - 188.2 (31.1)
AMP PEAK 12(8Q24.21) MUTATED 83 40 0.6 - 101.2 (22.6)
AMP PEAK 12(8Q24.21) WILD-TYPE 174 58 0.5 - 188.2 (34.9)

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

'amp_11q22.2' versus 'YEARS_TO_BIRTH'

P value = 0.00564 (Wilcoxon-test), Q value = 0.047

Table S36.  Gene #13: 'amp_11q22.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
AMP PEAK 13(11Q22.2) MUTATED 36 66.8 (14.3)
AMP PEAK 13(11Q22.2) WILD-TYPE 220 59.9 (14.6)

Figure S36.  Get High-res Image Gene #13: 'amp_11q22.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_12q15' versus 'Time to Death'

P value = 0.0594 (logrank test), Q value = 0.22

Table S37.  Gene #14: 'amp_12q15' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 257 98 0.5 - 188.2 (31.1)
AMP PEAK 14(12Q15) MUTATED 94 42 0.6 - 136.4 (31.7)
AMP PEAK 14(12Q15) WILD-TYPE 163 56 0.5 - 188.2 (30.8)

Figure S37.  Get High-res Image Gene #14: 'amp_12q15' versus Clinical Feature #1: 'Time to Death'

'amp_12q15' versus 'YEARS_TO_BIRTH'

P value = 0.00574 (Wilcoxon-test), Q value = 0.048

Table S38.  Gene #14: 'amp_12q15' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
AMP PEAK 14(12Q15) MUTATED 94 64.1 (13.7)
AMP PEAK 14(12Q15) WILD-TYPE 162 58.9 (15.0)

Figure S38.  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 = 0.001

Table S39.  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 44 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 35 4 1 2 6 1 1 26 3 1 2 4 1 4 2

Figure S39.  Get High-res Image Gene #14: 'amp_12q15' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'amp_12q15' versus 'GENDER'

P value = 0.000429 (Fisher's exact test), Q value = 0.0099

Table S40.  Gene #14: 'amp_12q15' versus Clinical Feature #4: 'GENDER'

nPatients FEMALE MALE
ALL 139 118
AMP PEAK 14(12Q15) MUTATED 37 57
AMP PEAK 14(12Q15) WILD-TYPE 102 61

Figure S40.  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 = 0.00062

Table S41.  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 24 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 15 19 1 2 6 13

Figure S41.  Get High-res Image Gene #14: 'amp_12q15' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'amp_12q15' versus 'RESIDUAL_TUMOR'

P value = 0.00116 (Fisher's exact test), Q value = 0.017

Table S42.  Gene #14: 'amp_12q15' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 152 69 9 26
AMP PEAK 14(12Q15) MUTATED 42 38 4 9
AMP PEAK 14(12Q15) WILD-TYPE 110 31 5 17

Figure S42.  Get High-res Image Gene #14: 'amp_12q15' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'amp_12q15' versus 'RACE'

P value = 0.00682 (Fisher's exact test), Q value = 0.055

Table S43.  Gene #14: 'amp_12q15' versus Clinical Feature #8: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 6 18 224
AMP PEAK 14(12Q15) MUTATED 3 1 86
AMP PEAK 14(12Q15) WILD-TYPE 3 17 138

Figure S43.  Get High-res Image Gene #14: 'amp_12q15' versus Clinical Feature #8: 'RACE'

'amp_13q34' versus 'TUMOR_TISSUE_SITE'

P value = 0.0537 (Fisher's exact test), Q value = 0.21

Table S44.  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 44 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 28 4 2 5 8 2 1 66 2 2 5 2 1 4 3

Figure S44.  Get High-res Image Gene #15: 'amp_13q34' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'amp_13q34' versus 'RADIATION_THERAPY'

P value = 0.0406 (Fisher's exact test), Q value = 0.17

Table S45.  Gene #15: 'amp_13q34' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 179 72
AMP PEAK 15(13Q34) MUTATED 32 22
AMP PEAK 15(13Q34) WILD-TYPE 147 50

Figure S45.  Get High-res Image Gene #15: 'amp_13q34' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_13q34' versus 'RACE'

P value = 0.0346 (Fisher's exact test), Q value = 0.16

Table S46.  Gene #15: 'amp_13q34' versus Clinical Feature #8: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 6 18 224
AMP PEAK 15(13Q34) MUTATED 0 8 45
AMP PEAK 15(13Q34) WILD-TYPE 6 10 179

Figure S46.  Get High-res Image Gene #15: 'amp_13q34' versus Clinical Feature #8: 'RACE'

'amp_15q26.3' versus 'YEARS_TO_BIRTH'

P value = 0.0157 (Wilcoxon-test), Q value = 0.093

Table S47.  Gene #16: 'amp_15q26.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
AMP PEAK 16(15Q26.3) MUTATED 83 63.7 (14.5)
AMP PEAK 16(15Q26.3) WILD-TYPE 173 59.4 (14.7)

Figure S47.  Get High-res Image Gene #16: 'amp_15q26.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_17p12' versus 'YEARS_TO_BIRTH'

P value = 0.0137 (Wilcoxon-test), Q value = 0.09

Table S48.  Gene #17: 'amp_17p12' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
AMP PEAK 17(17P12) MUTATED 101 63.8 (13.7)
AMP PEAK 17(17P12) WILD-TYPE 155 58.9 (15.1)

Figure S48.  Get High-res Image Gene #17: 'amp_17p12' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_17p12' versus 'RADIATION_THERAPY'

P value = 0.0459 (Fisher's exact test), Q value = 0.19

Table S49.  Gene #17: 'amp_17p12' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 179 72
AMP PEAK 17(17P12) MUTATED 64 36
AMP PEAK 17(17P12) WILD-TYPE 115 36

Figure S49.  Get High-res Image Gene #17: 'amp_17p12' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_17p12' versus 'HISTOLOGICAL_TYPE'

P value = 0.00385 (Fisher's exact test), Q value = 0.035

Table S50.  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 24 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 13 16 2 2 6 7

Figure S50.  Get High-res Image Gene #17: 'amp_17p12' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'amp_17p11.2' versus 'YEARS_TO_BIRTH'

P value = 0.015 (Wilcoxon-test), Q value = 0.093

Table S51.  Gene #18: 'amp_17p11.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
AMP PEAK 18(17P11.2) MUTATED 103 63.6 (13.8)
AMP PEAK 18(17P11.2) WILD-TYPE 153 59.0 (15.1)

Figure S51.  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 = 0.0445 (Fisher's exact test), Q value = 0.18

Table S52.  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 44 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 22 3 1 4 6 1 1 51 1 2 3 2 1 3 3

Figure S52.  Get High-res Image Gene #18: 'amp_17p11.2' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'amp_17p11.2' versus 'RADIATION_THERAPY'

P value = 0.000373 (Fisher's exact test), Q value = 0.0092

Table S53.  Gene #18: 'amp_17p11.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 179 72
AMP PEAK 18(17P11.2) MUTATED 60 42
AMP PEAK 18(17P11.2) WILD-TYPE 119 30

Figure S53.  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 = 0.001

Table S54.  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 24 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 11 12 2 2 6 6

Figure S54.  Get High-res Image Gene #18: 'amp_17p11.2' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'amp_17q24.3' versus 'YEARS_TO_BIRTH'

P value = 0.0336 (Wilcoxon-test), Q value = 0.15

Table S55.  Gene #19: 'amp_17q24.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
AMP PEAK 19(17Q24.3) MUTATED 78 63.8 (14.1)
AMP PEAK 19(17Q24.3) WILD-TYPE 178 59.5 (14.9)

Figure S55.  Get High-res Image Gene #19: 'amp_17q24.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_17q24.3' versus 'GENDER'

P value = 0.0299 (Fisher's exact test), Q value = 0.14

Table S56.  Gene #19: 'amp_17q24.3' versus Clinical Feature #4: 'GENDER'

nPatients FEMALE MALE
ALL 139 118
AMP PEAK 19(17Q24.3) MUTATED 51 28
AMP PEAK 19(17Q24.3) WILD-TYPE 88 90

Figure S56.  Get High-res Image Gene #19: 'amp_17q24.3' versus Clinical Feature #4: 'GENDER'

'amp_17q24.3' versus 'RADIATION_THERAPY'

P value = 0.0244 (Fisher's exact test), Q value = 0.13

Table S57.  Gene #19: 'amp_17q24.3' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 179 72
AMP PEAK 19(17Q24.3) MUTATED 48 30
AMP PEAK 19(17Q24.3) WILD-TYPE 131 42

Figure S57.  Get High-res Image Gene #19: 'amp_17q24.3' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_17q24.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.0139 (Fisher's exact test), Q value = 0.09

Table S58.  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 24 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 12 16 2 2 6 12

Figure S58.  Get High-res Image Gene #19: 'amp_17q24.3' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'amp_17q24.3' versus 'RESIDUAL_TUMOR'

P value = 0.0375 (Fisher's exact test), Q value = 0.16

Table S59.  Gene #19: 'amp_17q24.3' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 152 69 9 26
AMP PEAK 19(17Q24.3) MUTATED 42 18 5 13
AMP PEAK 19(17Q24.3) WILD-TYPE 110 51 4 13

Figure S59.  Get High-res Image Gene #19: 'amp_17q24.3' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'amp_19q12' versus 'YEARS_TO_BIRTH'

P value = 0.000522 (Wilcoxon-test), Q value = 0.011

Table S60.  Gene #21: 'amp_19q12' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
AMP PEAK 21(19Q12) MUTATED 92 64.8 (13.0)
AMP PEAK 21(19Q12) WILD-TYPE 164 58.6 (15.3)

Figure S60.  Get High-res Image Gene #21: 'amp_19q12' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_19q12' versus 'RADIATION_THERAPY'

P value = 0.0588 (Fisher's exact test), Q value = 0.22

Table S61.  Gene #21: 'amp_19q12' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 179 72
AMP PEAK 21(19Q12) MUTATED 58 33
AMP PEAK 21(19Q12) WILD-TYPE 121 39

Figure S61.  Get High-res Image Gene #21: 'amp_19q12' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_19q12' versus 'HISTOLOGICAL_TYPE'

P value = 0.0167 (Fisher's exact test), Q value = 0.096

Table S62.  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 24 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 10 12 2 2 6 11

Figure S62.  Get High-res Image Gene #21: 'amp_19q12' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'amp_20q13.33' versus 'Time to Death'

P value = 0.0219 (logrank test), Q value = 0.12

Table S63.  Gene #22: 'amp_20q13.33' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 257 98 0.5 - 188.2 (31.1)
AMP PEAK 22(20Q13.33) MUTATED 98 44 0.6 - 171.1 (24.4)
AMP PEAK 22(20Q13.33) WILD-TYPE 159 54 0.5 - 188.2 (34.9)

Figure S63.  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 = 0.000219 (Wilcoxon-test), Q value = 0.0065

Table S64.  Gene #22: 'amp_20q13.33' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
AMP PEAK 22(20Q13.33) MUTATED 98 65.2 (13.4)
AMP PEAK 22(20Q13.33) WILD-TYPE 158 58.1 (14.9)

Figure S64.  Get High-res Image Gene #22: 'amp_20q13.33' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_20q13.33' versus 'GENDER'

P value = 0.0142 (Fisher's exact test), Q value = 0.09

Table S65.  Gene #22: 'amp_20q13.33' versus Clinical Feature #4: 'GENDER'

nPatients FEMALE MALE
ALL 139 118
AMP PEAK 22(20Q13.33) MUTATED 43 55
AMP PEAK 22(20Q13.33) WILD-TYPE 96 63

Figure S65.  Get High-res Image Gene #22: 'amp_20q13.33' versus Clinical Feature #4: 'GENDER'

'amp_20q13.33' versus 'RADIATION_THERAPY'

P value = 0.00948 (Fisher's exact test), Q value = 0.068

Table S66.  Gene #22: 'amp_20q13.33' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 179 72
AMP PEAK 22(20Q13.33) MUTATED 59 37
AMP PEAK 22(20Q13.33) WILD-TYPE 120 35

Figure S66.  Get High-res Image Gene #22: 'amp_20q13.33' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_20q13.33' versus 'HISTOLOGICAL_TYPE'

P value = 0.0012 (Fisher's exact test), Q value = 0.017

Table S67.  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 24 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 10 11 2 2 6 9

Figure S67.  Get High-res Image Gene #22: 'amp_20q13.33' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'amp_21q21.1' versus 'YEARS_TO_BIRTH'

P value = 0.00471 (Wilcoxon-test), Q value = 0.042

Table S68.  Gene #23: 'amp_21q21.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
AMP PEAK 23(21Q21.1) MUTATED 72 64.9 (11.7)
AMP PEAK 23(21Q21.1) WILD-TYPE 184 59.3 (15.5)

Figure S68.  Get High-res Image Gene #23: 'amp_21q21.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_xp21.2' versus 'YEARS_TO_BIRTH'

P value = 0.0291 (Wilcoxon-test), Q value = 0.14

Table S69.  Gene #24: 'amp_xp21.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
AMP PEAK 24(XP21.2) MUTATED 96 63.6 (12.7)
AMP PEAK 24(XP21.2) WILD-TYPE 160 59.2 (15.6)

Figure S69.  Get High-res Image Gene #24: 'amp_xp21.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_xp21.2' versus 'RADIATION_THERAPY'

P value = 0.0212 (Fisher's exact test), Q value = 0.12

Table S70.  Gene #24: 'amp_xp21.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 179 72
AMP PEAK 24(XP21.2) MUTATED 60 36
AMP PEAK 24(XP21.2) WILD-TYPE 119 36

Figure S70.  Get High-res Image Gene #24: 'amp_xp21.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

'amp_xp21.2' versus 'HISTOLOGICAL_TYPE'

P value = 0.00892 (Fisher's exact test), Q value = 0.066

Table S71.  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 24 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 12 15 2 2 6 7

Figure S71.  Get High-res Image Gene #24: 'amp_xp21.2' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'amp_xq21.1' versus 'YEARS_TO_BIRTH'

P value = 0.0497 (Wilcoxon-test), Q value = 0.2

Table S72.  Gene #25: 'amp_xq21.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
AMP PEAK 25(XQ21.1) MUTATED 46 64.5 (12.2)
AMP PEAK 25(XQ21.1) WILD-TYPE 210 60.0 (15.2)

Figure S72.  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 = 0.058 (logrank test), Q value = 0.22

Table S73.  Gene #26: 'del_1p36.32' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 257 98 0.5 - 188.2 (31.1)
DEL PEAK 1(1P36.32) MUTATED 69 24 0.7 - 188.2 (37.1)
DEL PEAK 1(1P36.32) WILD-TYPE 188 74 0.5 - 152.1 (27.9)

Figure S73.  Get High-res Image Gene #26: 'del_1p36.32' versus Clinical Feature #1: 'Time to Death'

'del_1p36.32' versus 'GENDER'

P value = 0.000385 (Fisher's exact test), Q value = 0.0092

Table S74.  Gene #26: 'del_1p36.32' versus Clinical Feature #4: 'GENDER'

nPatients FEMALE MALE
ALL 139 118
DEL PEAK 1(1P36.32) MUTATED 50 19
DEL PEAK 1(1P36.32) WILD-TYPE 89 99

Figure S74.  Get High-res Image Gene #26: 'del_1p36.32' versus Clinical Feature #4: 'GENDER'

'del_1p36.32' versus 'RADIATION_THERAPY'

P value = 0.0112 (Fisher's exact test), Q value = 0.077

Table S75.  Gene #26: 'del_1p36.32' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 179 72
DEL PEAK 1(1P36.32) MUTATED 56 11
DEL PEAK 1(1P36.32) WILD-TYPE 123 61

Figure S75.  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 = 0.00062

Table S76.  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 24 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 20 24 2 2 5 20

Figure S76.  Get High-res Image Gene #26: 'del_1p36.32' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_1q44' versus 'YEARS_TO_BIRTH'

P value = 0.00196 (Wilcoxon-test), Q value = 0.024

Table S77.  Gene #27: 'del_1q44' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
DEL PEAK 2(1Q44) MUTATED 80 65.0 (13.5)
DEL PEAK 2(1Q44) WILD-TYPE 176 58.9 (14.9)

Figure S77.  Get High-res Image Gene #27: 'del_1q44' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_1q44' versus 'RADIATION_THERAPY'

P value = 0.000919 (Fisher's exact test), Q value = 0.016

Table S78.  Gene #27: 'del_1q44' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 179 72
DEL PEAK 2(1Q44) MUTATED 45 34
DEL PEAK 2(1Q44) WILD-TYPE 134 38

Figure S78.  Get High-res Image Gene #27: 'del_1q44' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_1q44' versus 'HISTOLOGICAL_TYPE'

P value = 6e-05 (Fisher's exact test), Q value = 0.0025

Table S79.  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 24 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 14 12 2 2 6 8

Figure S79.  Get High-res Image Gene #27: 'del_1q44' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_2p25.3' versus 'YEARS_TO_BIRTH'

P value = 0.0551 (Wilcoxon-test), Q value = 0.21

Table S80.  Gene #28: 'del_2p25.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
DEL PEAK 3(2P25.3) MUTATED 93 63.5 (13.8)
DEL PEAK 3(2P25.3) WILD-TYPE 163 59.3 (15.1)

Figure S80.  Get High-res Image Gene #28: 'del_2p25.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_2p25.3' versus 'GENDER'

P value = 0.0195 (Fisher's exact test), Q value = 0.11

Table S81.  Gene #28: 'del_2p25.3' versus Clinical Feature #4: 'GENDER'

nPatients FEMALE MALE
ALL 139 118
DEL PEAK 3(2P25.3) MUTATED 60 34
DEL PEAK 3(2P25.3) WILD-TYPE 79 84

Figure S81.  Get High-res Image Gene #28: 'del_2p25.3' versus Clinical Feature #4: 'GENDER'

'del_2p25.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.00191 (Fisher's exact test), Q value = 0.024

Table S82.  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 24 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 12 15 2 2 6 13

Figure S82.  Get High-res Image Gene #28: 'del_2p25.3' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_2p25.3' versus 'RACE'

P value = 0.00241 (Fisher's exact test), Q value = 0.027

Table S83.  Gene #28: 'del_2p25.3' versus Clinical Feature #8: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 6 18 224
DEL PEAK 3(2P25.3) MUTATED 1 13 75
DEL PEAK 3(2P25.3) WILD-TYPE 5 5 149

Figure S83.  Get High-res Image Gene #28: 'del_2p25.3' versus Clinical Feature #8: 'RACE'

'del_2q37.3' versus 'Time to Death'

P value = 0.00698 (logrank test), Q value = 0.055

Table S84.  Gene #29: 'del_2q37.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 257 98 0.5 - 188.2 (31.1)
DEL PEAK 4(2Q37.3) MUTATED 108 51 1.1 - 106.5 (26.7)
DEL PEAK 4(2Q37.3) WILD-TYPE 149 47 0.5 - 188.2 (33.5)

Figure S84.  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 = 0.00718 (Wilcoxon-test), Q value = 0.056

Table S85.  Gene #29: 'del_2q37.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
DEL PEAK 4(2Q37.3) MUTATED 107 63.8 (13.9)
DEL PEAK 4(2Q37.3) WILD-TYPE 149 58.7 (15.0)

Figure S85.  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 = 0.0282 (Fisher's exact test), Q value = 0.14

Table S86.  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 44 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 21 3 1 5 5 2 0 47 3 0 3 2 1 4 2

Figure S86.  Get High-res Image Gene #29: 'del_2q37.3' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_2q37.3' versus 'RADIATION_THERAPY'

P value = 0.0159 (Fisher's exact test), Q value = 0.093

Table S87.  Gene #29: 'del_2q37.3' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 179 72
DEL PEAK 4(2Q37.3) MUTATED 66 39
DEL PEAK 4(2Q37.3) WILD-TYPE 113 33

Figure S87.  Get High-res Image Gene #29: 'del_2q37.3' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_2q37.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.00162 (Fisher's exact test), Q value = 0.021

Table S88.  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 24 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 9 10 2 2 6 10

Figure S88.  Get High-res Image Gene #29: 'del_2q37.3' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_2q37.3' versus 'Time to Death'

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

Table S89.  Gene #30: 'del_2q37.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 257 98 0.5 - 188.2 (31.1)
DEL PEAK 5(2Q37.3) MUTATED 110 50 1.1 - 171.1 (27.4)
DEL PEAK 5(2Q37.3) WILD-TYPE 147 48 0.5 - 188.2 (33.4)

Figure S89.  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 = 0.00219 (Wilcoxon-test), Q value = 0.025

Table S90.  Gene #30: 'del_2q37.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
DEL PEAK 5(2Q37.3) MUTATED 109 64.1 (13.9)
DEL PEAK 5(2Q37.3) WILD-TYPE 147 58.4 (14.9)

Figure S90.  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 = 0.00692 (Fisher's exact test), Q value = 0.055

Table S91.  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 44 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 22 3 1 5 5 2 0 44 3 0 2 2 1 4 2

Figure S91.  Get High-res Image Gene #30: 'del_2q37.3' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_2q37.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.00552 (Fisher's exact test), Q value = 0.047

Table S92.  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 24 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 9 11 2 2 6 9

Figure S92.  Get High-res Image Gene #30: 'del_2q37.3' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_3p21.31' versus 'RADIATION_THERAPY'

P value = 0.0382 (Fisher's exact test), Q value = 0.17

Table S93.  Gene #31: 'del_3p21.31' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 179 72
DEL PEAK 6(3P21.31) MUTATED 39 25
DEL PEAK 6(3P21.31) WILD-TYPE 140 47

Figure S93.  Get High-res Image Gene #31: 'del_3p21.31' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_3p21.31' versus 'HISTOLOGICAL_TYPE'

P value = 0.00097 (Fisher's exact test), Q value = 0.016

Table S94.  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 24 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 13 16 2 0 3 14

Figure S94.  Get High-res Image Gene #31: 'del_3p21.31' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_3q13.31' versus 'YEARS_TO_BIRTH'

P value = 0.0112 (Wilcoxon-test), Q value = 0.077

Table S95.  Gene #32: 'del_3q13.31' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
DEL PEAK 7(3Q13.31) MUTATED 50 64.7 (16.0)
DEL PEAK 7(3Q13.31) WILD-TYPE 206 59.9 (14.3)

Figure S95.  Get High-res Image Gene #32: 'del_3q13.31' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_3q13.31' versus 'RADIATION_THERAPY'

P value = 0.0238 (Fisher's exact test), Q value = 0.12

Table S96.  Gene #32: 'del_3q13.31' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 179 72
DEL PEAK 7(3Q13.31) MUTATED 29 21
DEL PEAK 7(3Q13.31) WILD-TYPE 150 51

Figure S96.  Get High-res Image Gene #32: 'del_3q13.31' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_4q35.1' versus 'YEARS_TO_BIRTH'

P value = 0.00166 (Wilcoxon-test), Q value = 0.021

Table S97.  Gene #34: 'del_4q35.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
DEL PEAK 9(4Q35.1) MUTATED 93 64.5 (15.0)
DEL PEAK 9(4Q35.1) WILD-TYPE 163 58.7 (14.2)

Figure S97.  Get High-res Image Gene #34: 'del_4q35.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_4q35.1' versus 'RADIATION_THERAPY'

P value = 0.00358 (Fisher's exact test), Q value = 0.033

Table S98.  Gene #34: 'del_4q35.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 179 72
DEL PEAK 9(4Q35.1) MUTATED 55 37
DEL PEAK 9(4Q35.1) WILD-TYPE 124 35

Figure S98.  Get High-res Image Gene #34: 'del_4q35.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_4q35.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.0115 (Fisher's exact test), Q value = 0.077

Table S99.  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 24 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 9 12 2 2 6 13

Figure S99.  Get High-res Image Gene #34: 'del_4q35.1' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_5p15.33' versus 'TUMOR_TISSUE_SITE'

P value = 0.0383 (Fisher's exact test), Q value = 0.17

Table S100.  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 44 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 38 4 1 5 7 2 1 67 3 1 4 2 1 7 3

Figure S100.  Get High-res Image Gene #35: 'del_5p15.33' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_6p25.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.0325 (Fisher's exact test), Q value = 0.15

Table S101.  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 24 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 17 21 2 2 6 15

Figure S101.  Get High-res Image Gene #36: 'del_6p25.3' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_6q14.1' versus 'TUMOR_TISSUE_SITE'

P value = 0.0254 (Fisher's exact test), Q value = 0.13

Table S102.  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 44 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 27 3 1 5 7 1 0 55 1 2 3 3 1 5 5

Figure S102.  Get High-res Image Gene #37: 'del_6q14.1' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_6q14.1' versus 'RADIATION_THERAPY'

P value = 0.0153 (Fisher's exact test), Q value = 0.093

Table S103.  Gene #37: 'del_6q14.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 179 72
DEL PEAK 12(6Q14.1) MUTATED 46 30
DEL PEAK 12(6Q14.1) WILD-TYPE 133 42

Figure S103.  Get High-res Image Gene #37: 'del_6q14.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_8p23.3' versus 'Time to Death'

P value = 0.0689 (logrank test), Q value = 0.24

Table S104.  Gene #39: 'del_8p23.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 257 98 0.5 - 188.2 (31.1)
DEL PEAK 14(8P23.3) MUTATED 81 36 0.6 - 171.1 (26.5)
DEL PEAK 14(8P23.3) WILD-TYPE 176 62 0.5 - 188.2 (32.7)

Figure S104.  Get High-res Image Gene #39: 'del_8p23.3' versus Clinical Feature #1: 'Time to Death'

'del_8p23.3' versus 'YEARS_TO_BIRTH'

P value = 0.0421 (Wilcoxon-test), Q value = 0.18

Table S105.  Gene #39: 'del_8p23.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
DEL PEAK 14(8P23.3) MUTATED 81 63.7 (13.3)
DEL PEAK 14(8P23.3) WILD-TYPE 175 59.5 (15.2)

Figure S105.  Get High-res Image Gene #39: 'del_8p23.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_8p23.3' versus 'RADIATION_THERAPY'

P value = 0.0524 (Fisher's exact test), Q value = 0.2

Table S106.  Gene #39: 'del_8p23.3' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 179 72
DEL PEAK 14(8P23.3) MUTATED 51 30
DEL PEAK 14(8P23.3) WILD-TYPE 128 42

Figure S106.  Get High-res Image Gene #39: 'del_8p23.3' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_9p24.3' versus 'YEARS_TO_BIRTH'

P value = 0.00116 (Wilcoxon-test), Q value = 0.017

Table S107.  Gene #40: 'del_9p24.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
DEL PEAK 15(9P24.3) MUTATED 100 64.8 (12.7)
DEL PEAK 15(9P24.3) WILD-TYPE 156 58.3 (15.4)

Figure S107.  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 = 0.0185 (logrank test), Q value = 0.1

Table S108.  Gene #41: 'del_9p21.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 257 98 0.5 - 188.2 (31.1)
DEL PEAK 16(9P21.3) MUTATED 114 53 0.6 - 188.2 (26.3)
DEL PEAK 16(9P21.3) WILD-TYPE 143 45 0.5 - 159.3 (34.4)

Figure S108.  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 = 0.0015 (Wilcoxon-test), Q value = 0.021

Table S109.  Gene #41: 'del_9p21.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
DEL PEAK 16(9P21.3) MUTATED 114 64.2 (13.2)
DEL PEAK 16(9P21.3) WILD-TYPE 142 58.1 (15.4)

Figure S109.  Get High-res Image Gene #41: 'del_9p21.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_9p21.3' versus 'HISTOLOGICAL_TYPE'

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

Table S110.  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 24 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 12 11 2 2 5 8

Figure S110.  Get High-res Image Gene #41: 'del_9p21.3' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_9q34.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.00063 (Fisher's exact test), Q value = 0.012

Table S111.  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 24 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 15 23 2 2 6 15

Figure S111.  Get High-res Image Gene #42: 'del_9q34.3' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_9q34.3' versus 'RESIDUAL_TUMOR'

P value = 0.00296 (Fisher's exact test), Q value = 0.031

Table S112.  Gene #42: 'del_9q34.3' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 152 69 9 26
DEL PEAK 17(9Q34.3) MUTATED 37 12 7 5
DEL PEAK 17(9Q34.3) WILD-TYPE 115 57 2 21

Figure S112.  Get High-res Image Gene #42: 'del_9q34.3' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'del_9q34.3' versus 'RACE'

P value = 0.0182 (Fisher's exact test), Q value = 0.1

Table S113.  Gene #42: 'del_9q34.3' versus Clinical Feature #8: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 6 18 224
DEL PEAK 17(9Q34.3) MUTATED 1 9 45
DEL PEAK 17(9Q34.3) WILD-TYPE 5 9 179

Figure S113.  Get High-res Image Gene #42: 'del_9q34.3' versus Clinical Feature #8: 'RACE'

'del_10p15.3' versus 'YEARS_TO_BIRTH'

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

Table S114.  Gene #43: 'del_10p15.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
DEL PEAK 18(10P15.3) MUTATED 127 62.8 (13.9)
DEL PEAK 18(10P15.3) WILD-TYPE 129 58.9 (15.3)

Figure S114.  Get High-res Image Gene #43: 'del_10p15.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_10p15.3' versus 'RADIATION_THERAPY'

P value = 0.0695 (Fisher's exact test), Q value = 0.24

Table S115.  Gene #43: 'del_10p15.3' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 179 72
DEL PEAK 18(10P15.3) MUTATED 83 43
DEL PEAK 18(10P15.3) WILD-TYPE 96 29

Figure S115.  Get High-res Image Gene #43: 'del_10p15.3' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_10p15.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.00012 (Fisher's exact test), Q value = 0.0039

Table S116.  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 24 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 10 16 2 2 5 6

Figure S116.  Get High-res Image Gene #43: 'del_10p15.3' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_10q23.31' versus 'YEARS_TO_BIRTH'

P value = 0.0157 (Wilcoxon-test), Q value = 0.093

Table S117.  Gene #44: 'del_10q23.31' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
DEL PEAK 19(10Q23.31) MUTATED 138 63.1 (13.0)
DEL PEAK 19(10Q23.31) WILD-TYPE 118 58.2 (16.2)

Figure S117.  Get High-res Image Gene #44: 'del_10q23.31' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_10q23.31' versus 'RADIATION_THERAPY'

P value = 0.0707 (Fisher's exact test), Q value = 0.25

Table S118.  Gene #44: 'del_10q23.31' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 179 72
DEL PEAK 19(10Q23.31) MUTATED 89 45
DEL PEAK 19(10Q23.31) WILD-TYPE 90 27

Figure S118.  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 = 0.00062

Table S119.  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 24 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 10 12 2 2 6 6

Figure S119.  Get High-res Image Gene #44: 'del_10q23.31' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_10q23.31' versus 'RACE'

P value = 0.0158 (Fisher's exact test), Q value = 0.093

Table S120.  Gene #44: 'del_10q23.31' versus Clinical Feature #8: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 6 18 224
DEL PEAK 19(10Q23.31) MUTATED 2 15 116
DEL PEAK 19(10Q23.31) WILD-TYPE 4 3 108

Figure S120.  Get High-res Image Gene #44: 'del_10q23.31' versus Clinical Feature #8: 'RACE'

'del_10q26.3' versus 'YEARS_TO_BIRTH'

P value = 0.00219 (Wilcoxon-test), Q value = 0.025

Table S121.  Gene #45: 'del_10q26.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
DEL PEAK 20(10Q26.3) MUTATED 131 63.8 (12.7)
DEL PEAK 20(10Q26.3) WILD-TYPE 125 57.7 (16.1)

Figure S121.  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 = 0.00062

Table S122.  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 24 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 10 14 2 2 6 6

Figure S122.  Get High-res Image Gene #45: 'del_10q26.3' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_10q26.3' versus 'RACE'

P value = 0.0649 (Fisher's exact test), Q value = 0.23

Table S123.  Gene #45: 'del_10q26.3' versus Clinical Feature #8: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 6 18 224
DEL PEAK 20(10Q26.3) MUTATED 3 14 110
DEL PEAK 20(10Q26.3) WILD-TYPE 3 4 114

Figure S123.  Get High-res Image Gene #45: 'del_10q26.3' versus Clinical Feature #8: 'RACE'

'del_11p15.5' versus 'YEARS_TO_BIRTH'

P value = 0.00335 (Wilcoxon-test), Q value = 0.032

Table S124.  Gene #46: 'del_11p15.5' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
DEL PEAK 21(11P15.5) MUTATED 109 63.8 (14.2)
DEL PEAK 21(11P15.5) WILD-TYPE 147 58.7 (14.8)

Figure S124.  Get High-res Image Gene #46: 'del_11p15.5' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_11p15.5' versus 'RADIATION_THERAPY'

P value = 0.0676 (Fisher's exact test), Q value = 0.24

Table S125.  Gene #46: 'del_11p15.5' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 179 72
DEL PEAK 21(11P15.5) MUTATED 71 38
DEL PEAK 21(11P15.5) WILD-TYPE 108 34

Figure S125.  Get High-res Image Gene #46: 'del_11p15.5' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_11q23.1' versus 'RADIATION_THERAPY'

P value = 0.0021 (Fisher's exact test), Q value = 0.025

Table S126.  Gene #47: 'del_11q23.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 179 72
DEL PEAK 22(11Q23.1) MUTATED 73 45
DEL PEAK 22(11Q23.1) WILD-TYPE 106 27

Figure S126.  Get High-res Image Gene #47: 'del_11q23.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_11q23.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.0225 (Fisher's exact test), Q value = 0.12

Table S127.  Gene #47: 'del_11q23.1' 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 24 28 2 2 6 21
DEL PEAK 22(11Q23.1) MUTATED 29 0 0 38 6 16 16 0 0 1 12
DEL PEAK 22(11Q23.1) WILD-TYPE 30 2 1 65 3 8 12 2 2 5 9

Figure S127.  Get High-res Image Gene #47: 'del_11q23.1' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_11q25' versus 'YEARS_TO_BIRTH'

P value = 0.00606 (Wilcoxon-test), Q value = 0.049

Table S128.  Gene #48: 'del_11q25' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
DEL PEAK 23(11Q25) MUTATED 122 63.5 (13.9)
DEL PEAK 23(11Q25) WILD-TYPE 134 58.4 (15.1)

Figure S128.  Get High-res Image Gene #48: 'del_11q25' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_11q25' versus 'RADIATION_THERAPY'

P value = 0.00775 (Fisher's exact test), Q value = 0.059

Table S129.  Gene #48: 'del_11q25' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 179 72
DEL PEAK 23(11Q25) MUTATED 77 45
DEL PEAK 23(11Q25) WILD-TYPE 102 27

Figure S129.  Get High-res Image Gene #48: 'del_11q25' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_11q25' versus 'HISTOLOGICAL_TYPE'

P value = 0.0017 (Fisher's exact test), Q value = 0.022

Table S130.  Gene #48: 'del_11q25' 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 24 28 2 2 6 21
DEL PEAK 23(11Q25) MUTATED 30 0 0 39 6 14 16 0 0 1 17
DEL PEAK 23(11Q25) WILD-TYPE 29 2 1 64 3 10 12 2 2 5 4

Figure S130.  Get High-res Image Gene #48: 'del_11q25' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_11q25' versus 'RESIDUAL_TUMOR'

P value = 0.0262 (Fisher's exact test), Q value = 0.13

Table S131.  Gene #48: 'del_11q25' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 152 69 9 26
DEL PEAK 23(11Q25) MUTATED 62 43 5 12
DEL PEAK 23(11Q25) WILD-TYPE 90 26 4 14

Figure S131.  Get High-res Image Gene #48: 'del_11q25' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'del_12p13.1' versus 'GENDER'

P value = 0.0353 (Fisher's exact test), Q value = 0.16

Table S132.  Gene #49: 'del_12p13.1' versus Clinical Feature #4: 'GENDER'

nPatients FEMALE MALE
ALL 139 118
DEL PEAK 24(12P13.1) MUTATED 39 48
DEL PEAK 24(12P13.1) WILD-TYPE 100 70

Figure S132.  Get High-res Image Gene #49: 'del_12p13.1' versus Clinical Feature #4: 'GENDER'

'del_12p13.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.0635 (Fisher's exact test), Q value = 0.23

Table S133.  Gene #49: '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 24 28 2 2 6 21
DEL PEAK 24(12P13.1) MUTATED 20 0 0 33 2 10 17 0 0 0 5
DEL PEAK 24(12P13.1) WILD-TYPE 39 2 1 70 7 14 11 2 2 6 16

Figure S133.  Get High-res Image Gene #49: 'del_12p13.1' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_12q12' versus 'Time to Death'

P value = 0.0181 (logrank test), Q value = 0.1

Table S134.  Gene #50: 'del_12q12' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 257 98 0.5 - 188.2 (31.1)
DEL PEAK 25(12Q12) MUTATED 56 28 1.1 - 86.1 (27.1)
DEL PEAK 25(12Q12) WILD-TYPE 201 70 0.5 - 188.2 (34.4)

Figure S134.  Get High-res Image Gene #50: 'del_12q12' versus Clinical Feature #1: 'Time to Death'

'del_12q12' versus 'RACE'

P value = 0.0357 (Fisher's exact test), Q value = 0.16

Table S135.  Gene #50: 'del_12q12' versus Clinical Feature #8: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 6 18 224
DEL PEAK 25(12Q12) MUTATED 0 8 45
DEL PEAK 25(12Q12) WILD-TYPE 6 10 179

Figure S135.  Get High-res Image Gene #50: 'del_12q12' versus Clinical Feature #8: 'RACE'

'del_12q24.33' versus 'YEARS_TO_BIRTH'

P value = 0.002 (Wilcoxon-test), Q value = 0.024

Table S136.  Gene #51: 'del_12q24.33' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
DEL PEAK 26(12Q24.33) MUTATED 70 65.4 (12.6)
DEL PEAK 26(12Q24.33) WILD-TYPE 186 59.1 (15.2)

Figure S136.  Get High-res Image Gene #51: 'del_12q24.33' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_13q14.2' versus 'YEARS_TO_BIRTH'

P value = 0.00129 (Wilcoxon-test), Q value = 0.018

Table S137.  Gene #52: 'del_13q14.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
DEL PEAK 27(13Q14.2) MUTATED 179 62.9 (13.5)
DEL PEAK 27(13Q14.2) WILD-TYPE 77 56.0 (16.4)

Figure S137.  Get High-res Image Gene #52: 'del_13q14.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_13q14.2' versus 'TUMOR_TISSUE_SITE'

P value = 0.0142 (Fisher's exact test), Q value = 0.09

Table S138.  Gene #52: '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 44 4 2 5 8 2 1 73 3 2 5 4 1 7 5
DEL PEAK 27(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 27(13Q14.2) WILD-TYPE 0 2 2 0 0 0 3 1 1 1 1 1 5 2 3 1 3 0 10 1 0 4 2 0 0 27 1 0 2 1 1 1 1

Figure S138.  Get High-res Image Gene #52: 'del_13q14.2' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_13q14.2' versus 'RADIATION_THERAPY'

P value = 0.0223 (Fisher's exact test), Q value = 0.12

Table S139.  Gene #52: 'del_13q14.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 179 72
DEL PEAK 27(13Q14.2) MUTATED 117 58
DEL PEAK 27(13Q14.2) WILD-TYPE 62 14

Figure S139.  Get High-res Image Gene #52: '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 = 0.00062

Table S140.  Gene #52: '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 24 28 2 2 6 21
DEL PEAK 27(13Q14.2) MUTATED 26 0 0 88 6 18 24 0 0 1 17
DEL PEAK 27(13Q14.2) WILD-TYPE 33 2 1 15 3 6 4 2 2 5 4

Figure S140.  Get High-res Image Gene #52: 'del_13q14.2' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_14q24.1' versus 'TUMOR_TISSUE_SITE'

P value = 0.0319 (Fisher's exact test), Q value = 0.15

Table S141.  Gene #53: '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 44 4 2 5 8 2 1 73 3 2 5 4 1 7 5
DEL PEAK 28(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 28(14Q24.1) WILD-TYPE 1 5 2 1 1 0 7 1 1 2 1 2 7 2 4 2 13 4 32 2 2 5 7 1 1 52 2 2 4 2 1 4 4

Figure S141.  Get High-res Image Gene #53: 'del_14q24.1' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_15q11.2' versus 'Time to Death'

P value = 0.00909 (logrank test), Q value = 0.066

Table S142.  Gene #54: 'del_15q11.2' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 257 98 0.5 - 188.2 (31.1)
DEL PEAK 29(15Q11.2) MUTATED 47 24 0.6 - 171.1 (21.3)
DEL PEAK 29(15Q11.2) WILD-TYPE 210 74 0.5 - 188.2 (33.0)

Figure S142.  Get High-res Image Gene #54: 'del_15q11.2' versus Clinical Feature #1: 'Time to Death'

'del_15q11.2' versus 'YEARS_TO_BIRTH'

P value = 0.000325 (Wilcoxon-test), Q value = 0.0088

Table S143.  Gene #54: 'del_15q11.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
DEL PEAK 29(15Q11.2) MUTATED 47 67.9 (12.2)
DEL PEAK 29(15Q11.2) WILD-TYPE 209 59.2 (14.8)

Figure S143.  Get High-res Image Gene #54: 'del_15q11.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_15q11.2' versus 'RACE'

P value = 0.0451 (Fisher's exact test), Q value = 0.18

Table S144.  Gene #54: 'del_15q11.2' versus Clinical Feature #8: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 6 18 224
DEL PEAK 29(15Q11.2) MUTATED 0 7 38
DEL PEAK 29(15Q11.2) WILD-TYPE 6 11 186

Figure S144.  Get High-res Image Gene #54: 'del_15q11.2' versus Clinical Feature #8: 'RACE'

'del_16q11.2' versus 'YEARS_TO_BIRTH'

P value = 0.0509 (Wilcoxon-test), Q value = 0.2

Table S145.  Gene #55: 'del_16q11.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
DEL PEAK 30(16Q11.2) MUTATED 130 62.6 (13.7)
DEL PEAK 30(16Q11.2) WILD-TYPE 126 59.0 (15.6)

Figure S145.  Get High-res Image Gene #55: 'del_16q11.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_16q11.2' versus 'TUMOR_TISSUE_SITE'

P value = 0.0593 (Fisher's exact test), Q value = 0.22

Table S146.  Gene #55: '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 44 4 2 5 8 2 1 73 3 2 5 4 1 7 5
DEL PEAK 30(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 30(16Q11.2) WILD-TYPE 0 4 2 0 1 0 10 1 1 2 1 0 4 2 2 1 6 3 15 4 1 4 3 2 1 45 1 1 4 1 0 3 1

Figure S146.  Get High-res Image Gene #55: '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 = 0.00062

Table S147.  Gene #55: '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 24 28 2 2 6 21
DEL PEAK 30(16Q11.2) MUTATED 13 0 0 66 3 10 20 0 1 0 17
DEL PEAK 30(16Q11.2) WILD-TYPE 46 2 1 37 6 14 8 2 1 6 4

Figure S147.  Get High-res Image Gene #55: 'del_16q11.2' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_16q11.2' versus 'RACE'

P value = 0.0126 (Fisher's exact test), Q value = 0.084

Table S148.  Gene #55: 'del_16q11.2' versus Clinical Feature #8: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 6 18 224
DEL PEAK 30(16Q11.2) MUTATED 1 14 109
DEL PEAK 30(16Q11.2) WILD-TYPE 5 4 115

Figure S148.  Get High-res Image Gene #55: 'del_16q11.2' versus Clinical Feature #8: 'RACE'

'del_16q23.1' versus 'YEARS_TO_BIRTH'

P value = 0.000198 (Wilcoxon-test), Q value = 0.0062

Table S149.  Gene #56: 'del_16q23.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
DEL PEAK 31(16Q23.1) MUTATED 133 64.2 (13.6)
DEL PEAK 31(16Q23.1) WILD-TYPE 123 57.2 (15.1)

Figure S149.  Get High-res Image Gene #56: 'del_16q23.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_16q23.1' versus 'TUMOR_TISSUE_SITE'

P value = 0.0307 (Fisher's exact test), Q value = 0.15

Table S150.  Gene #56: '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 44 4 2 5 8 2 1 73 3 2 5 4 1 7 5
DEL PEAK 31(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 31(16Q23.1) WILD-TYPE 0 4 2 0 1 0 9 1 1 2 1 0 4 2 2 1 3 2 19 4 1 3 3 2 1 44 1 0 4 1 0 3 1

Figure S150.  Get High-res Image Gene #56: '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 = 0.00062

Table S151.  Gene #56: '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 24 28 2 2 6 21
DEL PEAK 31(16Q23.1) MUTATED 14 0 0 68 2 13 18 0 1 0 18
DEL PEAK 31(16Q23.1) WILD-TYPE 45 2 1 35 7 11 10 2 1 6 3

Figure S151.  Get High-res Image Gene #56: 'del_16q23.1' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_17p13.1' versus 'TUMOR_TISSUE_SITE'

P value = 0.0635 (Fisher's exact test), Q value = 0.23

Table S152.  Gene #57: '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 44 4 2 5 8 2 1 73 3 2 5 4 1 7 5
DEL PEAK 32(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 32(17P13.1) WILD-TYPE 1 3 2 0 1 1 12 2 1 2 1 1 7 2 2 2 7 2 17 0 1 4 4 1 0 45 1 0 3 0 0 2 1

Figure S152.  Get High-res Image Gene #57: 'del_17p13.1' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_17p13.1' versus 'GENDER'

P value = 0.0455 (Fisher's exact test), Q value = 0.18

Table S153.  Gene #57: 'del_17p13.1' versus Clinical Feature #4: 'GENDER'

nPatients FEMALE MALE
ALL 139 118
DEL PEAK 32(17P13.1) MUTATED 78 51
DEL PEAK 32(17P13.1) WILD-TYPE 61 67

Figure S153.  Get High-res Image Gene #57: 'del_17p13.1' versus Clinical Feature #4: 'GENDER'

'del_17p13.1' versus 'RADIATION_THERAPY'

P value = 0.0503 (Fisher's exact test), Q value = 0.2

Table S154.  Gene #57: 'del_17p13.1' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 179 72
DEL PEAK 32(17P13.1) MUTATED 81 43
DEL PEAK 32(17P13.1) WILD-TYPE 98 29

Figure S154.  Get High-res Image Gene #57: '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 = 0.00062

Table S155.  Gene #57: '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 24 28 2 2 6 21
DEL PEAK 32(17P13.1) MUTATED 11 0 0 66 7 13 16 0 1 0 15
DEL PEAK 32(17P13.1) WILD-TYPE 48 2 1 37 2 11 12 2 1 6 6

Figure S155.  Get High-res Image Gene #57: 'del_17p13.1' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_17q11.2' versus 'YEARS_TO_BIRTH'

P value = 0.00312 (Wilcoxon-test), Q value = 0.031

Table S156.  Gene #58: 'del_17q11.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
DEL PEAK 33(17Q11.2) MUTATED 81 64.6 (14.5)
DEL PEAK 33(17Q11.2) WILD-TYPE 175 59.1 (14.6)

Figure S156.  Get High-res Image Gene #58: 'del_17q11.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_17q11.2' versus 'TUMOR_TISSUE_SITE'

P value = 8e-05 (Fisher's exact test), Q value = 0.0028

Table S157.  Gene #58: '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 44 4 2 5 8 2 1 73 3 2 5 4 1 7 5
DEL PEAK 33(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 33(17Q11.2) WILD-TYPE 0 1 2 1 2 1 24 2 1 2 1 1 10 2 3 2 10 0 24 3 2 4 6 2 0 55 3 0 4 0 1 3 3

Figure S157.  Get High-res Image Gene #58: 'del_17q11.2' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_17q11.2' versus 'RADIATION_THERAPY'

P value = 0.0105 (Fisher's exact test), Q value = 0.074

Table S158.  Gene #58: 'del_17q11.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 179 72
DEL PEAK 33(17Q11.2) MUTATED 48 32
DEL PEAK 33(17Q11.2) WILD-TYPE 131 40

Figure S158.  Get High-res Image Gene #58: 'del_17q11.2' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_17q11.2' versus 'HISTOLOGICAL_TYPE'

P value = 6e-04 (Fisher's exact test), Q value = 0.012

Table S159.  Gene #58: '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 24 28 2 2 6 21
DEL PEAK 33(17Q11.2) MUTATED 17 0 0 21 4 13 15 0 0 0 11
DEL PEAK 33(17Q11.2) WILD-TYPE 42 2 1 82 5 11 13 2 2 6 10

Figure S159.  Get High-res Image Gene #58: 'del_17q11.2' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_17q25.3' versus 'YEARS_TO_BIRTH'

P value = 0.00547 (Wilcoxon-test), Q value = 0.047

Table S160.  Gene #59: 'del_17q25.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
DEL PEAK 34(17Q25.3) MUTATED 66 64.7 (12.7)
DEL PEAK 34(17Q25.3) WILD-TYPE 190 59.5 (15.2)

Figure S160.  Get High-res Image Gene #59: 'del_17q25.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_18q23' versus 'Time to Death'

P value = 0.00342 (logrank test), Q value = 0.032

Table S161.  Gene #61: 'del_18q23' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 257 98 0.5 - 188.2 (31.1)
DEL PEAK 36(18Q23) MUTATED 86 43 0.6 - 188.2 (25.8)
DEL PEAK 36(18Q23) WILD-TYPE 171 55 0.5 - 159.3 (34.5)

Figure S161.  Get High-res Image Gene #61: 'del_18q23' versus Clinical Feature #1: 'Time to Death'

'del_18q23' versus 'YEARS_TO_BIRTH'

P value = 0.00262 (Wilcoxon-test), Q value = 0.028

Table S162.  Gene #61: 'del_18q23' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
DEL PEAK 36(18Q23) MUTATED 86 64.6 (14.4)
DEL PEAK 36(18Q23) WILD-TYPE 170 58.9 (14.6)

Figure S162.  Get High-res Image Gene #61: 'del_18q23' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_18q23' versus 'HISTOLOGICAL_TYPE'

P value = 0.0046 (Fisher's exact test), Q value = 0.041

Table S163.  Gene #61: '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 24 28 2 2 6 21
DEL PEAK 36(18Q23) MUTATED 16 0 0 28 6 9 15 0 0 0 12
DEL PEAK 36(18Q23) WILD-TYPE 43 2 1 75 3 15 13 2 2 6 9

Figure S163.  Get High-res Image Gene #61: 'del_18q23' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_19p13.3' versus 'GENDER'

P value = 0.0115 (Fisher's exact test), Q value = 0.077

Table S164.  Gene #62: 'del_19p13.3' versus Clinical Feature #4: 'GENDER'

nPatients FEMALE MALE
ALL 139 118
DEL PEAK 37(19P13.3) MUTATED 47 23
DEL PEAK 37(19P13.3) WILD-TYPE 92 95

Figure S164.  Get High-res Image Gene #62: 'del_19p13.3' versus Clinical Feature #4: 'GENDER'

'del_19p13.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.00244 (Fisher's exact test), Q value = 0.027

Table S165.  Gene #62: '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 24 28 2 2 6 21
DEL PEAK 37(19P13.3) MUTATED 6 0 0 43 3 6 7 0 0 0 5
DEL PEAK 37(19P13.3) WILD-TYPE 53 2 1 60 6 18 21 2 2 6 16

Figure S165.  Get High-res Image Gene #62: 'del_19p13.3' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_19q13.43' versus 'RADIATION_THERAPY'

P value = 0.0159 (Fisher's exact test), Q value = 0.093

Table S166.  Gene #63: 'del_19q13.43' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 179 72
DEL PEAK 38(19Q13.43) MUTATED 66 39
DEL PEAK 38(19Q13.43) WILD-TYPE 113 33

Figure S166.  Get High-res Image Gene #63: 'del_19q13.43' versus Clinical Feature #5: 'RADIATION_THERAPY'

'del_19q13.43' versus 'HISTOLOGICAL_TYPE'

P value = 0.00069 (Fisher's exact test), Q value = 0.013

Table S167.  Gene #63: '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 24 28 2 2 6 21
DEL PEAK 38(19Q13.43) MUTATED 17 0 0 43 5 8 18 0 0 0 15
DEL PEAK 38(19Q13.43) WILD-TYPE 42 2 1 60 4 16 10 2 2 6 6

Figure S167.  Get High-res Image Gene #63: 'del_19q13.43' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_21q11.2' versus 'HISTOLOGICAL_TYPE'

P value = 0.0534 (Fisher's exact test), Q value = 0.21

Table S168.  Gene #64: '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 24 28 2 2 6 21
DEL PEAK 39(21Q11.2) MUTATED 8 0 0 18 5 4 7 0 0 0 9
DEL PEAK 39(21Q11.2) WILD-TYPE 51 2 1 85 4 20 21 2 2 6 12

Figure S168.  Get High-res Image Gene #64: 'del_21q11.2' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_21q22.3' versus 'YEARS_TO_BIRTH'

P value = 0.000554 (Wilcoxon-test), Q value = 0.011

Table S169.  Gene #65: 'del_21q22.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
DEL PEAK 40(21Q22.3) MUTATED 66 66.3 (11.8)
DEL PEAK 40(21Q22.3) WILD-TYPE 190 58.9 (15.2)

Figure S169.  Get High-res Image Gene #65: 'del_21q22.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_22q13.32' versus 'GENDER'

P value = 0.062 (Fisher's exact test), Q value = 0.23

Table S170.  Gene #66: 'del_22q13.32' versus Clinical Feature #4: 'GENDER'

nPatients FEMALE MALE
ALL 139 118
DEL PEAK 41(22Q13.32) MUTATED 52 31
DEL PEAK 41(22Q13.32) WILD-TYPE 87 87

Figure S170.  Get High-res Image Gene #66: 'del_22q13.32' versus Clinical Feature #4: 'GENDER'

'del_xp21.1' versus 'YEARS_TO_BIRTH'

P value = 0.0265 (Wilcoxon-test), Q value = 0.13

Table S171.  Gene #67: 'del_xp21.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
DEL PEAK 42(XP21.1) MUTATED 55 57.1 (15.4)
DEL PEAK 42(XP21.1) WILD-TYPE 201 61.9 (14.4)

Figure S171.  Get High-res Image Gene #67: 'del_xp21.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_xp21.1' versus 'GENDER'

P value = 0.0672 (Fisher's exact test), Q value = 0.24

Table S172.  Gene #67: 'del_xp21.1' versus Clinical Feature #4: 'GENDER'

nPatients FEMALE MALE
ALL 139 118
DEL PEAK 42(XP21.1) MUTATED 36 19
DEL PEAK 42(XP21.1) WILD-TYPE 103 99

Figure S172.  Get High-res Image Gene #67: 'del_xp21.1' versus Clinical Feature #4: 'GENDER'

'del_xp21.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.0537 (Fisher's exact test), Q value = 0.21

Table S173.  Gene #67: '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 24 28 2 2 6 21
DEL PEAK 42(XP21.1) MUTATED 6 0 0 31 3 6 6 1 0 1 1
DEL PEAK 42(XP21.1) WILD-TYPE 53 2 1 72 6 18 22 1 2 5 20

Figure S173.  Get High-res Image Gene #67: 'del_xp21.1' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_xq21.1' versus 'Time to Death'

P value = 0.00318 (logrank test), Q value = 0.031

Table S174.  Gene #68: 'del_xq21.1' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 257 98 0.5 - 188.2 (31.1)
DEL PEAK 43(XQ21.1) MUTATED 114 33 1.4 - 188.2 (35.1)
DEL PEAK 43(XQ21.1) WILD-TYPE 143 65 0.5 - 159.3 (27.0)

Figure S174.  Get High-res Image Gene #68: 'del_xq21.1' versus Clinical Feature #1: 'Time to Death'

'del_xq21.1' versus 'GENDER'

P value = 0.0233 (Fisher's exact test), Q value = 0.12

Table S175.  Gene #68: 'del_xq21.1' versus Clinical Feature #4: 'GENDER'

nPatients FEMALE MALE
ALL 139 118
DEL PEAK 43(XQ21.1) MUTATED 71 43
DEL PEAK 43(XQ21.1) WILD-TYPE 68 75

Figure S175.  Get High-res Image Gene #68: 'del_xq21.1' versus Clinical Feature #4: 'GENDER'

'del_xq21.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.00062 (Fisher's exact test), Q value = 0.012

Table S176.  Gene #68: '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 24 28 2 2 6 21
DEL PEAK 43(XQ21.1) MUTATED 16 0 0 62 4 9 10 0 0 1 12
DEL PEAK 43(XQ21.1) WILD-TYPE 43 2 1 41 5 15 18 2 2 5 9

Figure S176.  Get High-res Image Gene #68: 'del_xq21.1' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_xq22.3' versus 'Time to Death'

P value = 0.00565 (logrank test), Q value = 0.047

Table S177.  Gene #69: 'del_xq22.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 257 98 0.5 - 188.2 (31.1)
DEL PEAK 44(XQ22.3) MUTATED 123 38 1.1 - 188.2 (35.3)
DEL PEAK 44(XQ22.3) WILD-TYPE 134 60 0.5 - 159.3 (26.7)

Figure S177.  Get High-res Image Gene #69: 'del_xq22.3' versus Clinical Feature #1: 'Time to Death'

'del_xq22.3' versus 'TUMOR_TISSUE_SITE'

P value = 0.00859 (Fisher's exact test), Q value = 0.064

Table S178.  Gene #69: '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 44 4 2 5 8 2 1 73 3 2 5 4 1 7 5
DEL PEAK 44(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 44(XQ22.3) WILD-TYPE 0 4 2 0 0 1 10 2 1 2 1 0 5 1 3 2 5 2 24 1 1 5 6 2 0 42 1 2 4 0 1 1 2

Figure S178.  Get High-res Image Gene #69: 'del_xq22.3' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_xq22.3' versus 'GENDER'

P value = 0.0448 (Fisher's exact test), Q value = 0.18

Table S179.  Gene #69: 'del_xq22.3' versus Clinical Feature #4: 'GENDER'

nPatients FEMALE MALE
ALL 139 118
DEL PEAK 44(XQ22.3) MUTATED 75 48
DEL PEAK 44(XQ22.3) WILD-TYPE 64 70

Figure S179.  Get High-res Image Gene #69: 'del_xq22.3' versus Clinical Feature #4: 'GENDER'

'del_xq22.3' versus 'HISTOLOGICAL_TYPE'

P value = 3e-05 (Fisher's exact test), Q value = 0.0013

Table S180.  Gene #69: '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 24 28 2 2 6 21
DEL PEAK 44(XQ22.3) MUTATED 15 0 0 66 4 9 15 0 0 1 13
DEL PEAK 44(XQ22.3) WILD-TYPE 44 2 1 37 5 15 13 2 2 5 8

Figure S180.  Get High-res Image Gene #69: 'del_xq22.3' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_xq22.3' versus 'RESIDUAL_TUMOR'

P value = 0.0596 (Fisher's exact test), Q value = 0.22

Table S181.  Gene #69: 'del_xq22.3' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 152 69 9 26
DEL PEAK 44(XQ22.3) MUTATED 81 31 3 7
DEL PEAK 44(XQ22.3) WILD-TYPE 71 38 6 19

Figure S181.  Get High-res Image Gene #69: '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/22534094/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/SARC-TP/22507207/SARC-TP.merged_data.txt

  • Number of patients = 257

  • Number of significantly focal cnvs = 69

  • 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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