Correlation between copy number variations of arm-level result and selected clinical features
Sarcoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1571BGT
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlation between copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1571BGT
Overview
Introduction

This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.

Summary

Testing the association between copy number variation 82 arm-level events and 9 clinical features across 257 patients, 125 significant findings detected with Q value < 0.25.

  • 1p gain cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • 1q gain cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 2p gain cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 2q gain cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 3p gain cnv correlated to 'TUMOR_TISSUE_SITE' and 'HISTOLOGICAL_TYPE'.

  • 3q gain cnv correlated to 'YEARS_TO_BIRTH' and 'HISTOLOGICAL_TYPE'.

  • 4p gain cnv correlated to 'HISTOLOGICAL_TYPE' and 'RESIDUAL_TUMOR'.

  • 4q gain cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 5p gain cnv correlated to 'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.

  • 5q gain cnv correlated to 'YEARS_TO_BIRTH' and 'TUMOR_TISSUE_SITE'.

  • 6p gain cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH', and 'HISTOLOGICAL_TYPE'.

  • 6q gain cnv correlated to 'Time to Death'.

  • 7p gain cnv correlated to 'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.

  • 7q gain cnv correlated to 'YEARS_TO_BIRTH',  'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.

  • 8p gain cnv correlated to 'Time to Death',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • 8q gain cnv correlated to 'Time to Death'.

  • 9p gain cnv correlated to 'YEARS_TO_BIRTH' and 'HISTOLOGICAL_TYPE'.

  • 9q gain cnv correlated to 'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE', and 'HISTOLOGICAL_TYPE'.

  • 10p gain cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 10q gain cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 11p gain cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH', and 'HISTOLOGICAL_TYPE'.

  • 11q gain cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.

  • 12p gain cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH', and 'HISTOLOGICAL_TYPE'.

  • 12q gain cnv correlated to 'RADIATION_THERAPY',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • 13q gain cnv correlated to 'RACE'.

  • 14q gain cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH', and 'TUMOR_TISSUE_SITE'.

  • 16p gain cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH', and 'HISTOLOGICAL_TYPE'.

  • 17p gain cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.

  • 17q gain cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 18p gain cnv correlated to 'YEARS_TO_BIRTH' and 'RADIATION_THERAPY'.

  • 18q gain cnv correlated to 'YEARS_TO_BIRTH'.

  • 19p gain cnv correlated to 'YEARS_TO_BIRTH' and 'HISTOLOGICAL_TYPE'.

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

  • 20p gain cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.

  • 20q gain cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'GENDER', and 'HISTOLOGICAL_TYPE'.

  • 21q gain cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.

  • 22q gain cnv correlated to 'YEARS_TO_BIRTH',  'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.

  • xp gain cnv correlated to 'HISTOLOGICAL_TYPE'.

  • xq gain cnv correlated to 'ETHNICITY'.

  • 1p loss cnv correlated to 'GENDER'.

  • 2p loss cnv correlated to 'YEARS_TO_BIRTH',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • 2q loss cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.

  • 3p loss cnv correlated to 'YEARS_TO_BIRTH' and 'HISTOLOGICAL_TYPE'.

  • 3q loss cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.

  • 4p loss cnv correlated to 'RESIDUAL_TUMOR'.

  • 5p loss cnv correlated to 'RESIDUAL_TUMOR'.

  • 5q loss cnv correlated to 'RESIDUAL_TUMOR'.

  • 6p loss cnv correlated to 'Time to Death'.

  • 8q loss cnv correlated to 'YEARS_TO_BIRTH'.

  • 9p loss cnv correlated to 'YEARS_TO_BIRTH'.

  • 9q loss cnv correlated to 'Time to Death'.

  • 10p loss cnv correlated to 'YEARS_TO_BIRTH',  'GENDER', and 'HISTOLOGICAL_TYPE'.

  • 10q loss cnv correlated to 'YEARS_TO_BIRTH',  'GENDER', and 'HISTOLOGICAL_TYPE'.

  • 11q loss cnv correlated to 'RADIATION_THERAPY'.

  • 13q loss cnv correlated to 'YEARS_TO_BIRTH' and 'HISTOLOGICAL_TYPE'.

  • 15q loss cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.

  • 16p loss cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 16q loss cnv correlated to 'YEARS_TO_BIRTH' and 'HISTOLOGICAL_TYPE'.

  • 17q loss cnv correlated to 'YEARS_TO_BIRTH' and 'RADIATION_THERAPY'.

  • 19p loss cnv correlated to 'RADIATION_THERAPY'.

  • 20p loss cnv correlated to 'YEARS_TO_BIRTH' and 'RADIATION_THERAPY'.

  • 20q loss cnv correlated to 'YEARS_TO_BIRTH' and 'RESIDUAL_TUMOR'.

  • 21q loss cnv correlated to 'YEARS_TO_BIRTH'.

  • 22q loss cnv correlated to 'GENDER'.

  • xq loss cnv correlated to 'HISTOLOGICAL_TYPE'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 82 arm-level events and 9 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 125 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
1p gain 59 (23%) 198 0.00149
(0.0422) 		0.0383
(0.231) 		0.016
(0.145) 		0.555
(0.85) 		0.0499
(0.279) 		0.0088
(0.11) 		0.505
(0.814) 		0.0367
(0.226) 		0.592
(0.859)
5p gain 98 (38%) 159 0.385
(0.723) 		0.000777
(0.0273) 		0.00397
(0.0696) 		0.609
(0.866) 		0.0222
(0.172) 		0.00535
(0.0845) 		0.58
(0.859) 		0.769
(0.976) 		1
(1.00)
7p gain 82 (32%) 175 0.237
(0.591) 		6.06e-06
(0.000922) 		0.0231
(0.172) 		0.894
(1.00) 		0.0112
(0.117) 		1e-05
(0.000922) 		0.895
(1.00) 		0.456
(0.783) 		0.656
(0.9)
20q gain 83 (32%) 174 0.00218
(0.0537) 		0.00019
(0.00878) 		0.194
(0.522) 		0.0108
(0.117) 		0.101
(0.385) 		0.00928
(0.11) 		0.291
(0.654) 		0.664
(0.9) 		1
(1.00)
6p gain 52 (20%) 205 0.000457
(0.0177) 		0.00643
(0.0949) 		0.823
(1.00) 		0.353
(0.702) 		0.0821
(0.35) 		0.0221
(0.172) 		0.733
(0.959) 		0.686
(0.917) 		1
(1.00)
7q gain 67 (26%) 190 0.378
(0.717) 		9.57e-07
(0.000353) 		0.0515
(0.281) 		0.255
(0.615) 		0.00666
(0.0963) 		0.00374
(0.0696) 		0.562
(0.853) 		0.791
(0.989) 		0.119
(0.416)
8p gain 52 (20%) 205 0.00961
(0.11) 		0.0603
(0.301) 		0.184
(0.51) 		1
(1.00) 		0.117
(0.413) 		0.0415
(0.245) 		0.0765
(0.34) 		0.0252
(0.184) 		0.29
(0.653)
9q gain 71 (28%) 186 0.877
(1.00) 		7.14e-07
(0.000353) 		0.00751
(0.103) 		0.263
(0.616) 		0.437
(0.77) 		3e-05
(0.00246) 		0.358
(0.706) 		0.801
(0.994) 		1
(1.00)
11p gain 23 (9%) 234 0.0053
(0.0845) 		4.29e-05
(0.00317) 		0.653
(0.9) 		0.52
(0.828) 		0.0844
(0.35) 		0.0223
(0.172) 		0.251
(0.615) 		0.258
(0.616) 		1
(1.00)
12p gain 41 (16%) 216 0.00398
(0.0696) 		0.000106
(0.00672) 		0.0676
(0.312) 		1
(1.00) 		0.258
(0.616) 		0.00114
(0.0366) 		0.656
(0.9) 		0.0528
(0.284) 		0.165
(0.486)
12q gain 31 (12%) 226 0.485
(0.81) 		0.139
(0.445) 		0.0843
(0.35) 		0.179
(0.504) 		0.0356
(0.223) 		0.00018
(0.00878) 		0.564
(0.853) 		0.00949
(0.11) 		0.103
(0.385)
14q gain 56 (22%) 201 0.00909
(0.11) 		0.0114
(0.117) 		0.0114
(0.117) 		0.651
(0.9) 		0.0643
(0.308) 		0.104
(0.385) 		0.944
(1.00) 		0.825
(1.00) 		1
(1.00)
16p gain 40 (16%) 217 0.0254
(0.184) 		0.0129
(0.129) 		0.753
(0.975) 		0.607
(0.866) 		0.345
(0.701) 		0.0289
(0.201) 		0.662
(0.9) 		0.491
(0.81) 		1
(1.00)
22q gain 58 (23%) 199 0.261
(0.616) 		0.00346
(0.0691) 		0.375
(0.714) 		0.656
(0.9) 		0.00718
(0.1) 		0.0301
(0.202) 		0.524
(0.828) 		0.841
(1.00) 		0.0866
(0.355)
2p loss 92 (36%) 165 0.133
(0.431) 		0.00246
(0.0573) 		0.418
(0.76) 		0.193
(0.522) 		0.384
(0.723) 		0.015
(0.142) 		0.659
(0.9) 		0.0304
(0.202) 		0.161
(0.48)
10p loss 121 (47%) 136 0.58
(0.859) 		0.0116
(0.117) 		0.37
(0.713) 		0.00406
(0.0696) 		0.0709
(0.323) 		1e-05
(0.000922) 		0.803
(0.994) 		0.0491
(0.277) 		0.371
(0.714)
10q loss 131 (51%) 126 0.302
(0.665) 		0.0108
(0.117) 		0.188
(0.519) 		0.00597
(0.0917) 		0.127
(0.428) 		1e-05
(0.000922) 		0.919
(1.00) 		0.11
(0.399) 		0.194
(0.522)
3p gain 38 (15%) 219 0.563
(0.853) 		0.0678
(0.312) 		0.0112
(0.117) 		0.29
(0.653) 		0.439
(0.77) 		0.00088
(0.0295) 		1
(1.00) 		0.0453
(0.266) 		1
(1.00)
3q gain 35 (14%) 222 0.319
(0.689) 		0.027
(0.193) 		0.0492
(0.277) 		0.28
(0.636) 		0.234
(0.586) 		0.00395
(0.0696) 		0.772
(0.976) 		0.0895
(0.363) 		1
(1.00)
4p gain 69 (27%) 188 0.0798
(0.346) 		0.619
(0.875) 		0.11
(0.399) 		0.325
(0.693) 		0.212
(0.555) 		0.00175
(0.0478) 		0.0132
(0.129) 		0.857
(1.00) 		1
(1.00)
5q gain 72 (28%) 185 0.18
(0.504) 		0.0221
(0.172) 		0.00467
(0.0783) 		0.407
(0.754) 		0.28
(0.636) 		0.489
(0.81) 		0.255
(0.615) 		0.333
(0.7) 		1
(1.00)
9p gain 53 (21%) 204 0.132
(0.431) 		0.000109
(0.00672) 		0.528
(0.83) 		0.0899
(0.363) 		0.608
(0.866) 		0.00766
(0.103) 		0.722
(0.951) 		0.527
(0.83) 		1
(1.00)
11q gain 21 (8%) 236 0.00986
(0.11) 		0.00538
(0.0845) 		0.733
(0.959) 		0.823
(1.00) 		0.139
(0.445) 		0.0736
(0.33) 		0.341
(0.7) 		0.624
(0.88) 		1
(1.00)
17p gain 61 (24%) 196 0.0357
(0.223) 		0.0311
(0.205) 		0.845
(1.00) 		0.771
(0.976) 		0.103
(0.385) 		0.0568
(0.298) 		0.0906
(0.363) 		0.225
(0.574) 		1
(1.00)
18p gain 52 (20%) 205 0.098
(0.379) 		0.00923
(0.11) 		0.766
(0.976) 		0.276
(0.63) 		0.00309
(0.0691) 		0.0458
(0.266) 		1
(1.00) 		0.334
(0.7) 		0.586
(0.859)
19p gain 88 (34%) 169 0.0737
(0.33) 		0.000296
(0.0128) 		0.489
(0.81) 		0.149
(0.464) 		0.769
(0.976) 		0.0223
(0.172) 		0.263
(0.616) 		0.502
(0.814) 		0.344
(0.701)
19q gain 64 (25%) 193 0.446
(0.774) 		0.00806
(0.106) 		0.256
(0.615) 		0.314
(0.683) 		0.147
(0.459) 		0.0346
(0.222) 		0.836
(1.00) 		0.848
(1.00) 		1
(1.00)
20p gain 62 (24%) 195 0.000343
(0.0141) 		0.00966
(0.11) 		0.839
(1.00) 		0.0591
(0.298) 		1
(1.00) 		0.455
(0.783) 		0.514
(0.825) 		0.355
(0.703) 		1
(1.00)
21q gain 59 (23%) 198 0.0145
(0.139) 		0.0171
(0.154) 		0.0589
(0.298) 		0.298
(0.658) 		1
(1.00) 		0.121
(0.416) 		0.339
(0.7) 		0.0574
(0.298) 		0.594
(0.859)
2q loss 75 (29%) 182 0.00121
(0.0372) 		0.000119
(0.00676) 		0.13
(0.431) 		0.494
(0.812) 		0.36
(0.707) 		0.14
(0.446) 		0.779
(0.977) 		0.102
(0.385) 		0.325
(0.693)
3p loss 56 (22%) 201 0.0647
(0.308) 		0.0368
(0.226) 		0.201
(0.538) 		1
(1.00) 		0.092
(0.367) 		0.00681
(0.0966) 		0.46
(0.784) 		0.913
(1.00) 		1
(1.00)
3q loss 51 (20%) 206 0.0083
(0.106) 		0.0229
(0.172) 		0.433
(0.77) 		0.161
(0.48) 		0.223
(0.571) 		0.124
(0.421) 		0.212
(0.555) 		0.817
(1.00) 		1
(1.00)
13q loss 132 (51%) 125 0.404
(0.751) 		0.0013
(0.0384) 		0.791
(0.989) 		0.0614
(0.302) 		0.264
(0.616) 		0.016
(0.145) 		0.475
(0.801) 		1
(1.00) 		0.671
(0.906)
15q loss 46 (18%) 211 0.000728
(0.0269) 		0.0186
(0.162) 		0.0681
(0.312) 		0.625
(0.88) 		0.367
(0.713) 		0.677
(0.909) 		0.873
(1.00) 		0.292
(0.654) 		0.588
(0.859)
16q loss 124 (48%) 133 0.0964
(0.374) 		0.00214
(0.0537) 		0.0604
(0.301) 		0.103
(0.385) 		0.577
(0.859) 		1e-05
(0.000922) 		0.408
(0.755) 		0.0813
(0.35) 		1
(1.00)
17q loss 49 (19%) 208 0.123
(0.42) 		0.0251
(0.184) 		0.503
(0.814) 		0.431
(0.77) 		0.00385
(0.0696) 		0.225
(0.574) 		0.804
(0.994) 		0.342
(0.7) 		0.586
(0.859)
20p loss 55 (21%) 202 0.547
(0.848) 		0.0032
(0.0691) 		0.0788
(0.344) 		0.362
(0.707) 		0.0184
(0.161) 		0.212
(0.555) 		0.0652
(0.308) 		0.588
(0.859) 		1
(1.00)
20q loss 25 (10%) 232 0.755
(0.976) 		0.0209
(0.172) 		0.0492
(0.277) 		0.399
(0.743) 		0.243
(0.599) 		0.492
(0.81) 		0.0348
(0.222) 		0.461
(0.784) 		1
(1.00)
1q gain 51 (20%) 206 0.518
(0.827) 		0.212
(0.555) 		0.362
(0.707) 		0.116
(0.412) 		0.864
(1.00) 		0.0188
(0.162) 		0.941
(1.00) 		0.902
(1.00) 		0.586
(0.859)
2p gain 22 (9%) 235 0.536
(0.837) 		0.255
(0.615) 		0.411
(0.758) 		0.661
(0.9) 		0.806
(0.994) 		0.021
(0.172) 		0.107
(0.394) 		0.651
(0.9) 		0.375
(0.714)
2q gain 22 (9%) 235 0.427
(0.768) 		0.35
(0.702) 		0.742
(0.966) 		0.186
(0.514) 		0.806
(0.994) 		0.00329
(0.0691) 		0.596
(0.86) 		0.439
(0.77) 		0.375
(0.714)
4q gain 48 (19%) 209 0.166
(0.486) 		0.418
(0.76) 		0.597
(0.86) 		0.873
(1.00) 		0.215
(0.56) 		0.0083
(0.106) 		0.369
(0.713) 		1
(1.00) 		1
(1.00)
6q gain 49 (19%) 208 0.0282
(0.198) 		0.0648
(0.308) 		0.93
(1.00) 		0.156
(0.476) 		0.156
(0.476) 		0.197
(0.528) 		0.839
(1.00) 		0.549
(0.848) 		1
(1.00)
8q gain 66 (26%) 191 0.00248
(0.0573) 		0.387
(0.726) 		0.0516
(0.281) 		0.568
(0.857) 		0.524
(0.828) 		0.0717
(0.325) 		0.488
(0.81) 		0.0656
(0.308) 		0.119
(0.416)
10p gain 22 (9%) 235 0.422
(0.763) 		0.771
(0.976) 		0.528
(0.83) 		0.661
(0.9) 		0.806
(0.994) 		0.0205
(0.172) 		0.672
(0.907) 		1
(1.00) 		1
(1.00)
10q gain 11 (4%) 246 0.331
(0.699) 		0.848
(1.00) 		0.543
(0.844) 		0.759
(0.976) 		1
(1.00) 		0.0155
(0.145) 		0.295
(0.656) 		1
(1.00) 		1
(1.00)
13q gain 15 (6%) 242 0.342
(0.7) 		0.614
(0.871) 		0.562
(0.853) 		0.0588
(0.298) 		0.769
(0.976) 		0.0834
(0.35) 		0.38
(0.718) 		0.0226
(0.172) 		1
(1.00)
17q gain 56 (22%) 201 0.532
(0.833) 		0.169
(0.488) 		0.48
(0.806) 		0.0961
(0.374) 		0.312
(0.682) 		0.00615
(0.0926) 		0.229
(0.579) 		0.12
(0.416) 		0.336
(0.7)
18q gain 37 (14%) 220 0.295
(0.656) 		0.0315
(0.206) 		0.664
(0.9) 		0.212
(0.555) 		0.847
(1.00) 		0.44
(0.77) 		0.44
(0.77) 		0.397
(0.741) 		1
(1.00)
xp gain 74 (29%) 183 0.27
(0.627) 		0.0646
(0.308) 		0.242
(0.599) 		0.128
(0.43) 		0.445
(0.774) 		0.03
(0.202) 		0.338
(0.7) 		1
(1.00) 		0.176
(0.501)
xq gain 34 (13%) 223 0.935
(1.00) 		0.538
(0.838) 		0.368
(0.713) 		0.584
(0.859) 		0.415
(0.76) 		0.274
(0.629) 		0.337
(0.7) 		1
(1.00) 		0.0179
(0.159)
1p loss 32 (12%) 225 0.0609
(0.302) 		0.142
(0.449) 		0.588
(0.859) 		0.0132
(0.129) 		1
(1.00) 		0.319
(0.689) 		0.474
(0.801) 		0.29
(0.653) 		1
(1.00)
4p loss 41 (16%) 216 0.322
(0.693) 		0.109
(0.399) 		0.815
(1.00) 		0.609
(0.866) 		0.055
(0.292) 		0.517
(0.827) 		0.03
(0.202) 		0.262
(0.616) 		1
(1.00)
5p loss 23 (9%) 234 0.212
(0.555) 		0.626
(0.88) 		0.428
(0.768) 		0.131
(0.431) 		0.332
(0.7) 		0.18
(0.504) 		0.0385
(0.231) 		0.242
(0.599) 		1
(1.00)
5q loss 34 (13%) 223 0.163
(0.484) 		0.115
(0.409) 		0.341
(0.7) 		0.361
(0.707) 		0.221
(0.57) 		0.136
(0.439) 		0.0228
(0.172) 		0.491
(0.81) 		1
(1.00)
6p loss 60 (23%) 197 0.00347
(0.0691) 		0.893
(1.00) 		0.901
(1.00) 		0.305
(0.668) 		0.744
(0.966) 		0.327
(0.694) 		0.555
(0.85) 		0.703
(0.933) 		1
(1.00)
8q loss 45 (18%) 212 0.88
(1.00) 		0.0399
(0.237) 		0.868
(1.00) 		0.414
(0.76) 		0.27
(0.627) 		0.414
(0.76) 		0.921
(1.00) 		0.136
(0.439) 		0.588
(0.859)
9p loss 82 (32%) 175 0.0656
(0.308) 		0.00215
(0.0537) 		0.131
(0.431) 		0.229
(0.579) 		0.456
(0.783) 		0.604
(0.866) 		0.0882
(0.359) 		0.419
(0.76) 		1
(1.00)
9q loss 50 (19%) 207 0.0375
(0.229) 		0.143
(0.45) 		0.83
(1.00) 		0.636
(0.89) 		0.862
(1.00) 		0.548
(0.848) 		0.178
(0.502) 		0.114
(0.408) 		1
(1.00)
11q loss 93 (36%) 164 0.641
(0.894) 		0.931
(1.00) 		0.909
(1.00) 		0.697
(0.929) 		0.0206
(0.172) 		0.218
(0.564) 		0.555
(0.85) 		0.774
(0.976) 		0.164
(0.485)
16p loss 75 (29%) 182 0.156
(0.476) 		0.166
(0.486) 		0.514
(0.825) 		0.168
(0.488) 		0.445
(0.774) 		1e-05
(0.000922) 		0.866
(1.00) 		0.132
(0.431) 		1
(1.00)
19p loss 24 (9%) 233 0.64
(0.894) 		0.491
(0.81) 		0.466
(0.79) 		1
(1.00) 		0.0299
(0.202) 		0.418
(0.76) 		0.19
(0.52) 		0.677
(0.909) 		1
(1.00)
21q loss 50 (19%) 207 0.38
(0.718) 		0.0277
(0.197) 		0.96
(1.00) 		1
(1.00) 		0.223
(0.571) 		0.0467
(0.269) 		0.251
(0.615) 		0.906
(1.00) 		1
(1.00)
22q loss 67 (26%) 190 0.924
(1.00) 		0.0821
(0.35) 		0.505
(0.814) 		0.0324
(0.21) 		1
(1.00) 		0.346
(0.701) 		0.458
(0.784) 		1
(1.00) 		0.338
(0.7)
xq loss 102 (40%) 155 0.46
(0.784) 		0.94
(1.00) 		0.262
(0.616) 		0.0964
(0.374) 		1
(1.00) 		0.00017
(0.00878) 		0.709
(0.938) 		0.353
(0.702) 		0.16
(0.48)
15q gain 62 (24%) 195 0.439
(0.77) 		0.0503
(0.279) 		0.423
(0.763) 		0.0787
(0.344) 		0.259
(0.616) 		0.355
(0.703) 		0.878
(1.00) 		0.655
(0.9) 		0.1
(0.384)
16q gain 19 (7%) 238 0.663
(0.9) 		0.504
(0.814) 		0.882
(1.00) 		0.236
(0.59) 		0.193
(0.522) 		0.523
(0.828) 		0.77
(0.976) 		1
(1.00) 		1
(1.00)
1q loss 40 (16%) 217 0.892
(1.00) 		0.177
(0.502) 		0.983
(1.00) 		0.731
(0.959) 		0.055
(0.292) 		0.159
(0.48) 		0.907
(1.00) 		0.707
(0.936) 		0.563
(0.853)
4q loss 50 (19%) 207 0.579
(0.859) 		0.152
(0.471) 		0.774
(0.976) 		0.154
(0.476) 		0.112
(0.403) 		0.629
(0.883) 		0.273
(0.629) 		0.438
(0.77) 		0.587
(0.859)
6q loss 52 (20%) 205 0.303
(0.666) 		0.765
(0.976) 		0.685
(0.917) 		0.276
(0.63) 		0.171
(0.492) 		0.118
(0.413) 		0.728
(0.958) 		1
(1.00) 		1
(1.00)
7p loss 32 (12%) 225 0.799
(0.994) 		0.349
(0.701) 		0.873
(1.00) 		0.129
(0.431) 		0.834
(1.00) 		0.712
(0.94) 		0.605
(0.866) 		0.173
(0.494) 		1
(1.00)
7q loss 36 (14%) 221 0.0865
(0.355) 		0.272
(0.629) 		0.888
(1.00) 		0.471
(0.797) 		0.693
(0.925) 		0.837
(1.00) 		0.804
(0.994) 		0.892
(1.00) 		1
(1.00)
8p loss 62 (24%) 195 0.0825
(0.35) 		0.439
(0.77) 		0.564
(0.853) 		0.77
(0.976) 		1
(1.00) 		0.903
(1.00) 		0.67
(0.906) 		0.126
(0.428) 		0.591
(0.859)
11p loss 96 (37%) 161 0.324
(0.693) 		0.348
(0.701) 		0.807
(0.994) 		0.607
(0.866) 		0.0845
(0.35) 		0.651
(0.9) 		0.504
(0.814) 		0.872
(1.00) 		0.159
(0.48)
12p loss 67 (26%) 190 0.736
(0.961) 		0.168
(0.488) 		0.907
(1.00) 		0.57
(0.858) 		0.75
(0.973) 		0.0776
(0.343) 		0.89
(1.00) 		0.183
(0.51) 		0.327
(0.694)
12q loss 59 (23%) 198 0.888
(1.00) 		0.171
(0.492) 		0.871
(1.00) 		0.555
(0.85) 		1
(1.00) 		0.376
(0.714) 		0.702
(0.933) 		0.121
(0.416) 		0.594
(0.859)
14q loss 62 (24%) 195 0.103
(0.385) 		0.483
(0.81) 		0.533
(0.833) 		1
(1.00) 		0.87
(1.00) 		0.849
(1.00) 		0.496
(0.812) 		0.779
(0.977) 		0.592
(0.859)
17p loss 57 (22%) 200 0.316
(0.685) 		0.0959
(0.374) 		0.617
(0.873) 		1
(1.00) 		0.231
(0.583) 		0.364
(0.709) 		0.932
(1.00) 		0.439
(0.77) 		1
(1.00)
18p loss 61 (24%) 196 0.0957
(0.374) 		0.348
(0.701) 		0.961
(1.00) 		0.771
(0.976) 		0.252
(0.615) 		0.831
(1.00) 		0.963
(1.00) 		1
(1.00) 		1
(1.00)
18q loss 69 (27%) 188 0.0518
(0.281) 		0.0567
(0.298) 		0.297
(0.658) 		0.778
(0.977) 		0.0588
(0.298) 		0.0662
(0.309) 		0.743
(0.966) 		0.927
(1.00) 		1
(1.00)
19q loss 41 (16%) 216 0.521
(0.828) 		0.585
(0.859) 		0.814
(1.00) 		0.865
(1.00) 		0.451
(0.781) 		0.353
(0.702) 		0.496
(0.812) 		0.497
(0.812) 		0.217
(0.563)
xp loss 63 (25%) 194 0.676
(0.909) 		0.253
(0.615) 		0.453
(0.783) 		0.19
(0.52) 		1
(1.00) 		0.11
(0.399) 		0.912
(1.00) 		0.145
(0.455) 		0.591
(0.859)
'1p gain' versus 'Time to Death'

P value = 0.00149 (logrank test), Q value = 0.042

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

nPatients nDeath Duration Range (Median), Month
ALL 257 98 0.5 - 188.2 (31.1)
1P GAIN MUTATED 59 31 1.1 - 106.5 (23.4)
1P GAIN WILD-TYPE 198 67 0.5 - 188.2 (33.4)

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

'1p gain' versus 'YEARS_TO_BIRTH'

P value = 0.0383 (Wilcoxon-test), Q value = 0.23

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

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
1P GAIN MUTATED 59 64.1 (13.7)
1P GAIN WILD-TYPE 197 59.9 (14.9)

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

'1p gain' versus 'TUMOR_TISSUE_SITE'

P value = 0.016 (Fisher's exact test), Q value = 0.15

Table S3.  Gene #1: '1p gain' 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
1P GAIN MUTATED 0 2 1 0 0 0 8 1 0 0 0 1 1 0 0 1 7 2 17 0 1 0 2 1 1 6 0 1 0 2 0 2 2
1P GAIN WILD-TYPE 1 5 1 1 2 1 20 1 1 2 1 1 9 2 4 1 10 3 27 4 1 5 6 1 0 67 3 1 5 2 1 5 3

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

'1p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0088 (Fisher's exact test), Q value = 0.11

Table S4.  Gene #1: '1p gain' 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
1P GAIN MUTATED 5 0 0 25 1 7 12 1 0 0 8
1P GAIN WILD-TYPE 54 2 1 78 8 17 16 1 2 6 13

Figure S4.  Get High-res Image Gene #1: '1p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'1p gain' versus 'RACE'

P value = 0.0367 (Fisher's exact test), Q value = 0.23

Table S5.  Gene #1: '1p gain' versus Clinical Feature #8: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 6 18 224
1P GAIN MUTATED 0 8 48
1P GAIN WILD-TYPE 6 10 176

Figure S5.  Get High-res Image Gene #1: '1p gain' versus Clinical Feature #8: 'RACE'

'1q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0188 (Fisher's exact test), Q value = 0.16

Table S6.  Gene #2: '1q gain' 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
1Q GAIN MUTATED 3 0 0 30 1 5 7 1 0 0 4
1Q GAIN WILD-TYPE 56 2 1 73 8 19 21 1 2 6 17

Figure S6.  Get High-res Image Gene #2: '1q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'2p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.021 (Fisher's exact test), Q value = 0.17

Table S7.  Gene #3: '2p gain' 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
2P GAIN MUTATED 7 0 0 4 3 2 5 1 0 0 0
2P GAIN WILD-TYPE 52 2 1 99 6 22 23 1 2 6 21

Figure S7.  Get High-res Image Gene #3: '2p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'2q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00329 (Fisher's exact test), Q value = 0.069

Table S8.  Gene #4: '2q gain' 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
2Q GAIN MUTATED 7 0 0 3 4 3 4 1 0 0 0
2Q GAIN WILD-TYPE 52 2 1 100 5 21 24 1 2 6 21

Figure S8.  Get High-res Image Gene #4: '2q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'3p gain' versus 'TUMOR_TISSUE_SITE'

P value = 0.0112 (Fisher's exact test), Q value = 0.12

Table S9.  Gene #5: '3p gain' 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
3P GAIN MUTATED 0 1 0 0 0 0 4 1 0 0 0 1 0 1 0 1 3 0 16 1 1 0 0 0 0 3 0 1 1 0 0 2 1
3P GAIN WILD-TYPE 1 6 2 1 2 1 24 1 1 2 1 1 10 1 4 1 14 5 28 3 1 5 8 2 1 70 3 1 4 4 1 5 4

Figure S9.  Get High-res Image Gene #5: '3p gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'3p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00088 (Fisher's exact test), Q value = 0.03

Table S10.  Gene #5: '3p gain' 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
3P GAIN MUTATED 1 0 0 17 0 3 11 0 0 0 6
3P GAIN WILD-TYPE 58 2 1 86 9 21 17 2 2 6 15

Figure S10.  Get High-res Image Gene #5: '3p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'3q gain' versus 'YEARS_TO_BIRTH'

P value = 0.027 (Wilcoxon-test), Q value = 0.19

Table S11.  Gene #6: '3q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
3Q GAIN MUTATED 35 65.9 (13.5)
3Q GAIN WILD-TYPE 221 60.0 (14.8)

Figure S11.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'3q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00395 (Fisher's exact test), Q value = 0.07

Table S12.  Gene #6: '3q gain' 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
3Q GAIN MUTATED 1 0 0 15 0 4 10 0 0 0 5
3Q GAIN WILD-TYPE 58 2 1 88 9 20 18 2 2 6 16

Figure S12.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'4p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00175 (Fisher's exact test), Q value = 0.048

Table S13.  Gene #7: '4p gain' 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
4P GAIN MUTATED 9 0 0 23 4 9 10 1 0 0 13
4P GAIN WILD-TYPE 50 2 1 80 5 15 18 1 2 6 8

Figure S13.  Get High-res Image Gene #7: '4p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'4p gain' versus 'RESIDUAL_TUMOR'

P value = 0.0132 (Fisher's exact test), Q value = 0.13

Table S14.  Gene #7: '4p gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 152 69 9 26
4P GAIN MUTATED 36 17 1 14
4P GAIN WILD-TYPE 116 52 8 12

Figure S14.  Get High-res Image Gene #7: '4p gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'4q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0083 (Fisher's exact test), Q value = 0.11

Table S15.  Gene #8: '4q gain' 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
4Q GAIN MUTATED 6 0 0 16 2 4 8 1 0 0 11
4Q GAIN WILD-TYPE 53 2 1 87 7 20 20 1 2 6 10

Figure S15.  Get High-res Image Gene #8: '4q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'5p gain' versus 'YEARS_TO_BIRTH'

P value = 0.000777 (Wilcoxon-test), Q value = 0.027

Table S16.  Gene #9: '5p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
5P GAIN MUTATED 97 64.9 (12.8)
5P GAIN WILD-TYPE 159 58.3 (15.3)

Figure S16.  Get High-res Image Gene #9: '5p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'5p gain' versus 'TUMOR_TISSUE_SITE'

P value = 0.00397 (Fisher's exact test), Q value = 0.07

Table S17.  Gene #9: '5p gain' 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
5P GAIN MUTATED 0 2 0 0 0 0 8 2 0 1 0 2 1 1 0 0 6 4 24 0 1 1 4 1 1 27 0 0 2 2 0 7 1
5P GAIN WILD-TYPE 1 5 2 1 2 1 20 0 1 1 1 0 9 1 4 2 11 1 20 4 1 4 4 1 0 46 3 2 3 2 1 0 4

Figure S17.  Get High-res Image Gene #9: '5p gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'5p gain' versus 'RADIATION_THERAPY'

P value = 0.0222 (Fisher's exact test), Q value = 0.17

Table S18.  Gene #9: '5p gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 179 72
5P GAIN MUTATED 61 36
5P GAIN WILD-TYPE 118 36

Figure S18.  Get High-res Image Gene #9: '5p gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

'5p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00535 (Fisher's exact test), Q value = 0.085

Table S19.  Gene #9: '5p gain' 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
5P GAIN MUTATED 15 0 0 40 3 10 18 0 0 0 12
5P GAIN WILD-TYPE 44 2 1 63 6 14 10 2 2 6 9

Figure S19.  Get High-res Image Gene #9: '5p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'5q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0221 (Wilcoxon-test), Q value = 0.17

Table S20.  Gene #10: '5q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
5Q GAIN MUTATED 72 64.5 (13.4)
5Q GAIN WILD-TYPE 184 59.4 (15.0)

Figure S20.  Get High-res Image Gene #10: '5q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'5q gain' versus 'TUMOR_TISSUE_SITE'

P value = 0.00467 (Fisher's exact test), Q value = 0.078

Table S21.  Gene #10: '5q gain' 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
5Q GAIN MUTATED 0 1 0 0 0 0 7 2 0 1 0 2 1 1 0 0 2 4 18 0 1 1 4 1 1 16 0 0 1 1 0 6 1
5Q GAIN WILD-TYPE 1 6 2 1 2 1 21 0 1 1 1 0 9 1 4 2 15 1 26 4 1 4 4 1 0 57 3 2 4 3 1 1 4

Figure S21.  Get High-res Image Gene #10: '5q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'6p gain' versus 'Time to Death'

P value = 0.000457 (logrank test), Q value = 0.018

Table S22.  Gene #11: '6p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 257 98 0.5 - 188.2 (31.1)
6P GAIN MUTATED 52 30 0.6 - 171.1 (27.6)
6P GAIN WILD-TYPE 205 68 0.5 - 188.2 (32.0)

Figure S22.  Get High-res Image Gene #11: '6p gain' versus Clinical Feature #1: 'Time to Death'

'6p gain' versus 'YEARS_TO_BIRTH'

P value = 0.00643 (Wilcoxon-test), Q value = 0.095

Table S23.  Gene #11: '6p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
6P GAIN MUTATED 51 66.0 (13.1)
6P GAIN WILD-TYPE 205 59.5 (14.9)

Figure S23.  Get High-res Image Gene #11: '6p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'6p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0221 (Fisher's exact test), Q value = 0.17

Table S24.  Gene #11: '6p gain' 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
6P GAIN MUTATED 11 0 0 15 0 9 7 0 0 0 10
6P GAIN WILD-TYPE 48 2 1 88 9 15 21 2 2 6 11

Figure S24.  Get High-res Image Gene #11: '6p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'6q gain' versus 'Time to Death'

P value = 0.0282 (logrank test), Q value = 0.2

Table S25.  Gene #12: '6q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 257 98 0.5 - 188.2 (31.1)
6Q GAIN MUTATED 49 24 0.6 - 171.1 (32.7)
6Q GAIN WILD-TYPE 208 74 0.5 - 188.2 (31.0)

Figure S25.  Get High-res Image Gene #12: '6q gain' versus Clinical Feature #1: 'Time to Death'

'7p gain' versus 'YEARS_TO_BIRTH'

P value = 6.06e-06 (Wilcoxon-test), Q value = 0.00092

Table S26.  Gene #13: '7p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
7P GAIN MUTATED 81 66.6 (12.7)
7P GAIN WILD-TYPE 175 58.2 (14.9)

Figure S26.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'7p gain' versus 'TUMOR_TISSUE_SITE'

P value = 0.0231 (Fisher's exact test), Q value = 0.17

Table S27.  Gene #13: '7p gain' 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
7P GAIN MUTATED 0 5 0 0 1 1 7 1 0 0 0 1 4 0 0 0 11 2 16 1 0 1 2 0 0 15 0 2 2 2 0 5 3
7P GAIN WILD-TYPE 1 2 2 1 1 0 21 1 1 2 1 1 6 2 4 2 6 3 28 3 2 4 6 2 1 58 3 0 3 2 1 2 2

Figure S27.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'7p gain' versus 'RADIATION_THERAPY'

P value = 0.0112 (Fisher's exact test), Q value = 0.12

Table S28.  Gene #13: '7p gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 179 72
7P GAIN MUTATED 49 32
7P GAIN WILD-TYPE 130 40

Figure S28.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

'7p gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00092

Table S29.  Gene #13: '7p gain' 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
7P GAIN MUTATED 11 0 0 23 4 13 16 0 0 0 15
7P GAIN WILD-TYPE 48 2 1 80 5 11 12 2 2 6 6

Figure S29.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'7q gain' versus 'YEARS_TO_BIRTH'

P value = 9.57e-07 (Wilcoxon-test), Q value = 0.00035

Table S30.  Gene #14: '7q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
7Q GAIN MUTATED 67 68.1 (10.4)
7Q GAIN WILD-TYPE 189 58.2 (15.2)

Figure S30.  Get High-res Image Gene #14: '7q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'7q gain' versus 'RADIATION_THERAPY'

P value = 0.00666 (Fisher's exact test), Q value = 0.096

Table S31.  Gene #14: '7q gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 179 72
7Q GAIN MUTATED 38 28
7Q GAIN WILD-TYPE 141 44

Figure S31.  Get High-res Image Gene #14: '7q gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

'7q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00374 (Fisher's exact test), Q value = 0.07

Table S32.  Gene #14: '7q gain' 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
7Q GAIN MUTATED 11 0 0 20 2 9 14 0 0 0 11
7Q GAIN WILD-TYPE 48 2 1 83 7 15 14 2 2 6 10

Figure S32.  Get High-res Image Gene #14: '7q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'8p gain' versus 'Time to Death'

P value = 0.00961 (logrank test), Q value = 0.11

Table S33.  Gene #15: '8p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 257 98 0.5 - 188.2 (31.1)
8P GAIN MUTATED 52 25 1.1 - 106.5 (19.3)
8P GAIN WILD-TYPE 205 73 0.5 - 188.2 (33.5)

Figure S33.  Get High-res Image Gene #15: '8p gain' versus Clinical Feature #1: 'Time to Death'

'8p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0415 (Fisher's exact test), Q value = 0.25

Table S34.  Gene #15: '8p gain' 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
8P GAIN MUTATED 5 0 0 21 1 9 8 0 0 0 8
8P GAIN WILD-TYPE 54 2 1 82 8 15 20 2 2 6 13

Figure S34.  Get High-res Image Gene #15: '8p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'8p gain' versus 'RACE'

P value = 0.0252 (Fisher's exact test), Q value = 0.18

Table S35.  Gene #15: '8p gain' versus Clinical Feature #8: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 6 18 224
8P GAIN MUTATED 4 4 42
8P GAIN WILD-TYPE 2 14 182

Figure S35.  Get High-res Image Gene #15: '8p gain' versus Clinical Feature #8: 'RACE'

'8q gain' versus 'Time to Death'

P value = 0.00248 (logrank test), Q value = 0.057

Table S36.  Gene #16: '8q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 257 98 0.5 - 188.2 (31.1)
8Q GAIN MUTATED 66 33 0.6 - 106.5 (21.1)
8Q GAIN WILD-TYPE 191 65 0.5 - 188.2 (34.7)

Figure S36.  Get High-res Image Gene #16: '8q gain' versus Clinical Feature #1: 'Time to Death'

'9p gain' versus 'YEARS_TO_BIRTH'

P value = 0.000109 (Wilcoxon-test), Q value = 0.0067

Table S37.  Gene #17: '9p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
9P GAIN MUTATED 52 67.5 (13.6)
9P GAIN WILD-TYPE 204 59.1 (14.6)

Figure S37.  Get High-res Image Gene #17: '9p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'9p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00766 (Fisher's exact test), Q value = 0.1

Table S38.  Gene #17: '9p gain' 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
9P GAIN MUTATED 12 0 0 13 1 7 14 1 0 0 5
9P GAIN WILD-TYPE 47 2 1 90 8 17 14 1 2 6 16

Figure S38.  Get High-res Image Gene #17: '9p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'9q gain' versus 'YEARS_TO_BIRTH'

P value = 7.14e-07 (Wilcoxon-test), Q value = 0.00035

Table S39.  Gene #18: '9q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
9Q GAIN MUTATED 71 68.0 (13.3)
9Q GAIN WILD-TYPE 185 58.1 (14.4)

Figure S39.  Get High-res Image Gene #18: '9q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'9q gain' versus 'TUMOR_TISSUE_SITE'

P value = 0.00751 (Fisher's exact test), Q value = 0.1

Table S40.  Gene #18: '9q gain' 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
9Q GAIN MUTATED 0 3 0 0 0 0 1 0 0 0 0 1 4 0 1 0 7 2 20 1 1 0 0 1 0 17 0 2 2 1 0 3 4
9Q GAIN WILD-TYPE 1 4 2 1 2 1 27 2 1 2 1 1 6 2 3 2 10 3 24 3 1 5 8 1 1 56 3 0 3 3 1 4 1

Figure S40.  Get High-res Image Gene #18: '9q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'9q gain' versus 'HISTOLOGICAL_TYPE'

P value = 3e-05 (Fisher's exact test), Q value = 0.0025

Table S41.  Gene #18: '9q gain' 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
9Q GAIN MUTATED 17 0 0 16 1 9 19 1 0 0 8
9Q GAIN WILD-TYPE 42 2 1 87 8 15 9 1 2 6 13

Figure S41.  Get High-res Image Gene #18: '9q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'10p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0205 (Fisher's exact test), Q value = 0.17

Table S42.  Gene #19: '10p gain' 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
10P GAIN MUTATED 2 0 0 5 0 5 6 1 0 0 3
10P GAIN WILD-TYPE 57 2 1 98 9 19 22 1 2 6 18

Figure S42.  Get High-res Image Gene #19: '10p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'10q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0155 (Fisher's exact test), Q value = 0.14

Table S43.  Gene #20: '10q gain' 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
10Q GAIN MUTATED 3 0 0 1 0 1 5 1 0 0 0
10Q GAIN WILD-TYPE 56 2 1 102 9 23 23 1 2 6 21

Figure S43.  Get High-res Image Gene #20: '10q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'11p gain' versus 'Time to Death'

P value = 0.0053 (logrank test), Q value = 0.085

Table S44.  Gene #21: '11p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 257 98 0.5 - 188.2 (31.1)
11P GAIN MUTATED 23 14 1.1 - 123.8 (18.1)
11P GAIN WILD-TYPE 234 84 0.5 - 188.2 (32.7)

Figure S44.  Get High-res Image Gene #21: '11p gain' versus Clinical Feature #1: 'Time to Death'

'11p gain' versus 'YEARS_TO_BIRTH'

P value = 4.29e-05 (Wilcoxon-test), Q value = 0.0032

Table S45.  Gene #21: '11p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
11P GAIN MUTATED 23 72.0 (12.6)
11P GAIN WILD-TYPE 233 59.7 (14.5)

Figure S45.  Get High-res Image Gene #21: '11p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'11p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0223 (Fisher's exact test), Q value = 0.17

Table S46.  Gene #21: '11p gain' 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
11P GAIN MUTATED 4 0 0 4 1 6 7 0 0 0 1
11P GAIN WILD-TYPE 55 2 1 99 8 18 21 2 2 6 20

Figure S46.  Get High-res Image Gene #21: '11p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'11q gain' versus 'Time to Death'

P value = 0.00986 (logrank test), Q value = 0.11

Table S47.  Gene #22: '11q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 257 98 0.5 - 188.2 (31.1)
11Q GAIN MUTATED 21 13 1.1 - 123.8 (18.1)
11Q GAIN WILD-TYPE 236 85 0.5 - 188.2 (32.1)

Figure S47.  Get High-res Image Gene #22: '11q gain' versus Clinical Feature #1: 'Time to Death'

'11q gain' versus 'YEARS_TO_BIRTH'

P value = 0.00538 (Wilcoxon-test), Q value = 0.085

Table S48.  Gene #22: '11q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
11Q GAIN MUTATED 21 68.5 (14.9)
11Q GAIN WILD-TYPE 235 60.1 (14.6)

Figure S48.  Get High-res Image Gene #22: '11q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'12p gain' versus 'Time to Death'

P value = 0.00398 (logrank test), Q value = 0.07

Table S49.  Gene #23: '12p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 257 98 0.5 - 188.2 (31.1)
12P GAIN MUTATED 41 23 0.7 - 112.0 (19.4)
12P GAIN WILD-TYPE 216 75 0.5 - 188.2 (33.0)

Figure S49.  Get High-res Image Gene #23: '12p gain' versus Clinical Feature #1: 'Time to Death'

'12p gain' versus 'YEARS_TO_BIRTH'

P value = 0.000106 (Wilcoxon-test), Q value = 0.0067

Table S50.  Gene #23: '12p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
12P GAIN MUTATED 41 68.5 (13.2)
12P GAIN WILD-TYPE 215 59.4 (14.6)

Figure S50.  Get High-res Image Gene #23: '12p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'12p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00114 (Fisher's exact test), Q value = 0.037

Table S51.  Gene #23: '12p gain' 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
12P GAIN MUTATED 7 0 0 8 3 4 9 1 0 0 9
12P GAIN WILD-TYPE 52 2 1 95 6 20 19 1 2 6 12

Figure S51.  Get High-res Image Gene #23: '12p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'12q gain' versus 'RADIATION_THERAPY'

P value = 0.0356 (Fisher's exact test), Q value = 0.22

Table S52.  Gene #24: '12q gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 179 72
12Q GAIN MUTATED 17 14
12Q GAIN WILD-TYPE 162 58

Figure S52.  Get High-res Image Gene #24: '12q gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

'12q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00018 (Fisher's exact test), Q value = 0.0088

Table S53.  Gene #24: '12q gain' 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
12Q GAIN MUTATED 2 0 0 6 4 5 9 1 0 0 4
12Q GAIN WILD-TYPE 57 2 1 97 5 19 19 1 2 6 17

Figure S53.  Get High-res Image Gene #24: '12q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'12q gain' versus 'RACE'

P value = 0.00949 (Fisher's exact test), Q value = 0.11

Table S54.  Gene #24: '12q gain' versus Clinical Feature #8: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 6 18 224
12Q GAIN MUTATED 3 0 26
12Q GAIN WILD-TYPE 3 18 198

Figure S54.  Get High-res Image Gene #24: '12q gain' versus Clinical Feature #8: 'RACE'

'13q gain' versus 'RACE'

P value = 0.0226 (Fisher's exact test), Q value = 0.17

Table S55.  Gene #25: '13q gain' versus Clinical Feature #8: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 6 18 224
13Q GAIN MUTATED 0 4 10
13Q GAIN WILD-TYPE 6 14 214

Figure S55.  Get High-res Image Gene #25: '13q gain' versus Clinical Feature #8: 'RACE'

'14q gain' versus 'Time to Death'

P value = 0.00909 (logrank test), Q value = 0.11

Table S56.  Gene #26: '14q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 257 98 0.5 - 188.2 (31.1)
14Q GAIN MUTATED 56 30 0.6 - 136.4 (22.7)
14Q GAIN WILD-TYPE 201 68 0.5 - 188.2 (33.3)

Figure S56.  Get High-res Image Gene #26: '14q gain' versus Clinical Feature #1: 'Time to Death'

'14q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0114 (Wilcoxon-test), Q value = 0.12

Table S57.  Gene #26: '14q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
14Q GAIN MUTATED 56 65.2 (14.9)
14Q GAIN WILD-TYPE 200 59.6 (14.5)

Figure S57.  Get High-res Image Gene #26: '14q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'14q gain' versus 'TUMOR_TISSUE_SITE'

P value = 0.0114 (Fisher's exact test), Q value = 0.12

Table S58.  Gene #26: '14q gain' 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
14Q GAIN MUTATED 1 3 0 0 0 0 4 0 0 0 0 2 0 1 1 1 5 3 13 0 1 0 3 1 0 9 0 2 2 0 0 2 2
14Q GAIN WILD-TYPE 0 4 2 1 2 1 24 2 1 2 1 0 10 1 3 1 12 2 31 4 1 5 5 1 1 64 3 0 3 4 1 5 3

Figure S58.  Get High-res Image Gene #26: '14q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'16p gain' versus 'Time to Death'

P value = 0.0254 (logrank test), Q value = 0.18

Table S59.  Gene #28: '16p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 257 98 0.5 - 188.2 (31.1)
16P GAIN MUTATED 40 22 3.9 - 86.1 (29.1)
16P GAIN WILD-TYPE 217 76 0.5 - 188.2 (31.5)

Figure S59.  Get High-res Image Gene #28: '16p gain' versus Clinical Feature #1: 'Time to Death'

'16p gain' versus 'YEARS_TO_BIRTH'

P value = 0.0129 (Wilcoxon-test), Q value = 0.13

Table S60.  Gene #28: '16p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
16P GAIN MUTATED 40 66.2 (13.6)
16P GAIN WILD-TYPE 216 59.8 (14.8)

Figure S60.  Get High-res Image Gene #28: '16p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'16p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0289 (Fisher's exact test), Q value = 0.2

Table S61.  Gene #28: '16p gain' 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
16P GAIN MUTATED 10 0 0 13 0 7 10 0 0 0 0
16P GAIN WILD-TYPE 49 2 1 90 9 17 18 2 2 6 21

Figure S61.  Get High-res Image Gene #28: '16p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'17p gain' versus 'Time to Death'

P value = 0.0357 (logrank test), Q value = 0.22

Table S62.  Gene #30: '17p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 257 98 0.5 - 188.2 (31.1)
17P GAIN MUTATED 61 31 0.6 - 106.5 (26.5)
17P GAIN WILD-TYPE 196 67 0.5 - 188.2 (32.0)

Figure S62.  Get High-res Image Gene #30: '17p gain' versus Clinical Feature #1: 'Time to Death'

'17p gain' versus 'YEARS_TO_BIRTH'

P value = 0.0311 (Wilcoxon-test), Q value = 0.2

Table S63.  Gene #30: '17p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
17P GAIN MUTATED 60 64.7 (13.0)
17P GAIN WILD-TYPE 196 59.7 (15.1)

Figure S63.  Get High-res Image Gene #30: '17p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'17q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00615 (Fisher's exact test), Q value = 0.093

Table S64.  Gene #31: '17q gain' 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
17Q GAIN MUTATED 6 0 0 19 2 11 9 0 0 0 9
17Q GAIN WILD-TYPE 53 2 1 84 7 13 19 2 2 6 12

Figure S64.  Get High-res Image Gene #31: '17q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'18p gain' versus 'YEARS_TO_BIRTH'

P value = 0.00923 (Wilcoxon-test), Q value = 0.11

Table S65.  Gene #32: '18p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
18P GAIN MUTATED 52 65.5 (12.4)
18P GAIN WILD-TYPE 204 59.6 (15.1)

Figure S65.  Get High-res Image Gene #32: '18p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'18p gain' versus 'RADIATION_THERAPY'

P value = 0.00309 (Fisher's exact test), Q value = 0.069

Table S66.  Gene #32: '18p gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 179 72
18P GAIN MUTATED 28 24
18P GAIN WILD-TYPE 151 48

Figure S66.  Get High-res Image Gene #32: '18p gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

'18q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0315 (Wilcoxon-test), Q value = 0.21

Table S67.  Gene #33: '18q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
18Q GAIN MUTATED 36 65.4 (14.3)
18Q GAIN WILD-TYPE 220 60.1 (14.7)

Figure S67.  Get High-res Image Gene #33: '18q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'19p gain' versus 'YEARS_TO_BIRTH'

P value = 0.000296 (Wilcoxon-test), Q value = 0.013

Table S68.  Gene #34: '19p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
19P GAIN MUTATED 87 65.3 (12.8)
19P GAIN WILD-TYPE 169 58.5 (15.2)

Figure S68.  Get High-res Image Gene #34: '19p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'19p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0223 (Fisher's exact test), Q value = 0.17

Table S69.  Gene #34: '19p gain' 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
19P GAIN MUTATED 19 0 0 29 3 9 17 0 0 0 11
19P GAIN WILD-TYPE 40 2 1 74 6 15 11 2 2 6 10

Figure S69.  Get High-res Image Gene #34: '19p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'19q gain' versus 'YEARS_TO_BIRTH'

P value = 0.00806 (Wilcoxon-test), Q value = 0.11

Table S70.  Gene #35: '19q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
19Q GAIN MUTATED 63 65.3 (12.7)
19Q GAIN WILD-TYPE 193 59.4 (15.1)

Figure S70.  Get High-res Image Gene #35: '19q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'19q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0346 (Fisher's exact test), Q value = 0.22

Table S71.  Gene #35: '19q gain' 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
19Q GAIN MUTATED 14 0 0 20 0 11 11 0 0 0 8
19Q GAIN WILD-TYPE 45 2 1 83 9 13 17 2 2 6 13

Figure S71.  Get High-res Image Gene #35: '19q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'20p gain' versus 'Time to Death'

P value = 0.000343 (logrank test), Q value = 0.014

Table S72.  Gene #36: '20p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 257 98 0.5 - 188.2 (31.1)
20P GAIN MUTATED 62 33 0.6 - 106.5 (25.3)
20P GAIN WILD-TYPE 195 65 0.5 - 188.2 (33.4)

Figure S72.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #1: 'Time to Death'

'20p gain' versus 'YEARS_TO_BIRTH'

P value = 0.00966 (Wilcoxon-test), Q value = 0.11

Table S73.  Gene #36: '20p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
20P GAIN MUTATED 62 65.4 (13.8)
20P GAIN WILD-TYPE 194 59.4 (14.8)

Figure S73.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'20q gain' versus 'Time to Death'

P value = 0.00218 (logrank test), Q value = 0.054

Table S74.  Gene #37: '20q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 257 98 0.5 - 188.2 (31.1)
20Q GAIN MUTATED 83 42 0.6 - 171.1 (25.4)
20Q GAIN WILD-TYPE 174 56 0.5 - 188.2 (33.5)

Figure S74.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #1: 'Time to Death'

'20q gain' versus 'YEARS_TO_BIRTH'

P value = 0.00019 (Wilcoxon-test), Q value = 0.0088

Table S75.  Gene #37: '20q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
20Q GAIN MUTATED 83 65.9 (13.1)
20Q GAIN WILD-TYPE 173 58.4 (14.9)

Figure S75.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'20q gain' versus 'GENDER'

P value = 0.0108 (Fisher's exact test), Q value = 0.12

Table S76.  Gene #37: '20q gain' versus Clinical Feature #4: 'GENDER'

nPatients FEMALE MALE
ALL 139 118
20Q GAIN MUTATED 35 48
20Q GAIN WILD-TYPE 104 70

Figure S76.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #4: 'GENDER'

'20q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00928 (Fisher's exact test), Q value = 0.11

Table S77.  Gene #37: '20q gain' 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
20Q GAIN MUTATED 15 0 0 27 3 12 16 0 0 0 10
20Q GAIN WILD-TYPE 44 2 1 76 6 12 12 2 2 6 11

Figure S77.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'21q gain' versus 'Time to Death'

P value = 0.0145 (logrank test), Q value = 0.14

Table S78.  Gene #38: '21q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 257 98 0.5 - 188.2 (31.1)
21Q GAIN MUTATED 59 29 0.5 - 136.4 (26.4)
21Q GAIN WILD-TYPE 198 69 0.6 - 188.2 (32.7)

Figure S78.  Get High-res Image Gene #38: '21q gain' versus Clinical Feature #1: 'Time to Death'

'21q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0171 (Wilcoxon-test), Q value = 0.15

Table S79.  Gene #38: '21q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
21Q GAIN MUTATED 58 64.9 (12.0)
21Q GAIN WILD-TYPE 198 59.6 (15.3)

Figure S79.  Get High-res Image Gene #38: '21q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'22q gain' versus 'YEARS_TO_BIRTH'

P value = 0.00346 (Wilcoxon-test), Q value = 0.069

Table S80.  Gene #39: '22q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
22Q GAIN MUTATED 58 65.8 (12.9)
22Q GAIN WILD-TYPE 198 59.4 (15.0)

Figure S80.  Get High-res Image Gene #39: '22q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'22q gain' versus 'RADIATION_THERAPY'

P value = 0.00718 (Fisher's exact test), Q value = 0.1

Table S81.  Gene #39: '22q gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 179 72
22Q GAIN MUTATED 32 25
22Q GAIN WILD-TYPE 147 47

Figure S81.  Get High-res Image Gene #39: '22q gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

'22q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0301 (Fisher's exact test), Q value = 0.2

Table S82.  Gene #39: '22q gain' 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
22Q GAIN MUTATED 6 0 0 24 1 7 12 0 0 0 8
22Q GAIN WILD-TYPE 53 2 1 79 8 17 16 2 2 6 13

Figure S82.  Get High-res Image Gene #39: '22q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'xp gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.03 (Fisher's exact test), Q value = 0.2

Table S83.  Gene #40: 'xp gain' 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
XP GAIN MUTATED 11 0 0 28 1 11 12 1 0 0 10
XP GAIN WILD-TYPE 48 2 1 75 8 13 16 1 2 6 11

Figure S83.  Get High-res Image Gene #40: 'xp gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'xq gain' versus 'ETHNICITY'

P value = 0.0179 (Fisher's exact test), Q value = 0.16

Table S84.  Gene #41: 'xq gain' versus Clinical Feature #9: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 5 220
XQ GAIN MUTATED 3 27
XQ GAIN WILD-TYPE 2 193

Figure S84.  Get High-res Image Gene #41: 'xq gain' versus Clinical Feature #9: 'ETHNICITY'

'1p loss' versus 'GENDER'

P value = 0.0132 (Fisher's exact test), Q value = 0.13

Table S85.  Gene #42: '1p loss' versus Clinical Feature #4: 'GENDER'

nPatients FEMALE MALE
ALL 139 118
1P LOSS MUTATED 24 8
1P LOSS WILD-TYPE 115 110

Figure S85.  Get High-res Image Gene #42: '1p loss' versus Clinical Feature #4: 'GENDER'

'2p loss' versus 'YEARS_TO_BIRTH'

P value = 0.00246 (Wilcoxon-test), Q value = 0.057

Table S86.  Gene #44: '2p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
2P LOSS MUTATED 91 64.7 (13.5)
2P LOSS WILD-TYPE 165 58.7 (15.0)

Figure S86.  Get High-res Image Gene #44: '2p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'2p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.015 (Fisher's exact test), Q value = 0.14

Table S87.  Gene #44: '2p loss' 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
2P LOSS MUTATED 13 0 0 44 1 10 13 0 0 0 11
2P LOSS WILD-TYPE 46 2 1 59 8 14 15 2 2 6 10

Figure S87.  Get High-res Image Gene #44: '2p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'2p loss' versus 'RACE'

P value = 0.0304 (Fisher's exact test), Q value = 0.2

Table S88.  Gene #44: '2p loss' versus Clinical Feature #8: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 6 18 224
2P LOSS MUTATED 0 10 76
2P LOSS WILD-TYPE 6 8 148

Figure S88.  Get High-res Image Gene #44: '2p loss' versus Clinical Feature #8: 'RACE'

'2q loss' versus 'Time to Death'

P value = 0.00121 (logrank test), Q value = 0.037

Table S89.  Gene #45: '2q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 257 98 0.5 - 188.2 (31.1)
2Q LOSS MUTATED 75 36 0.7 - 106.5 (20.3)
2Q LOSS WILD-TYPE 182 62 0.5 - 188.2 (34.4)

Figure S89.  Get High-res Image Gene #45: '2q loss' versus Clinical Feature #1: 'Time to Death'

'2q loss' versus 'YEARS_TO_BIRTH'

P value = 0.000119 (Wilcoxon-test), Q value = 0.0068

Table S90.  Gene #45: '2q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
2Q LOSS MUTATED 74 66.3 (13.3)
2Q LOSS WILD-TYPE 182 58.6 (14.8)

Figure S90.  Get High-res Image Gene #45: '2q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'3p loss' versus 'YEARS_TO_BIRTH'

P value = 0.0368 (Wilcoxon-test), Q value = 0.23

Table S91.  Gene #46: '3p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
3P LOSS MUTATED 56 63.9 (15.6)
3P LOSS WILD-TYPE 200 60.0 (14.4)

Figure S91.  Get High-res Image Gene #46: '3p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'3p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00681 (Fisher's exact test), Q value = 0.097

Table S92.  Gene #46: '3p loss' 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
3P LOSS MUTATED 16 0 0 11 2 8 10 0 2 2 5
3P LOSS WILD-TYPE 43 2 1 92 7 16 18 2 0 4 16

Figure S92.  Get High-res Image Gene #46: '3p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'3q loss' versus 'Time to Death'

P value = 0.0083 (logrank test), Q value = 0.11

Table S93.  Gene #47: '3q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 257 98 0.5 - 188.2 (31.1)
3Q LOSS MUTATED 51 26 1.1 - 188.2 (23.4)
3Q LOSS WILD-TYPE 206 72 0.5 - 171.1 (33.0)

Figure S93.  Get High-res Image Gene #47: '3q loss' versus Clinical Feature #1: 'Time to Death'

'3q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0229 (Wilcoxon-test), Q value = 0.17

Table S94.  Gene #47: '3q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
3Q LOSS MUTATED 51 64.7 (14.8)
3Q LOSS WILD-TYPE 205 59.9 (14.6)

Figure S94.  Get High-res Image Gene #47: '3q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'4p loss' versus 'RESIDUAL_TUMOR'

P value = 0.03 (Fisher's exact test), Q value = 0.2

Table S95.  Gene #48: '4p loss' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 152 69 9 26
4P LOSS MUTATED 30 9 2 0
4P LOSS WILD-TYPE 122 60 7 26

Figure S95.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'5p loss' versus 'RESIDUAL_TUMOR'

P value = 0.0385 (Fisher's exact test), Q value = 0.23

Table S96.  Gene #50: '5p loss' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 152 69 9 26
5P LOSS MUTATED 11 10 2 0
5P LOSS WILD-TYPE 141 59 7 26

Figure S96.  Get High-res Image Gene #50: '5p loss' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'5q loss' versus 'RESIDUAL_TUMOR'

P value = 0.0228 (Fisher's exact test), Q value = 0.17

Table S97.  Gene #51: '5q loss' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 152 69 9 26
5Q LOSS MUTATED 19 12 3 0
5Q LOSS WILD-TYPE 133 57 6 26

Figure S97.  Get High-res Image Gene #51: '5q loss' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'6p loss' versus 'Time to Death'

P value = 0.00347 (logrank test), Q value = 0.069

Table S98.  Gene #52: '6p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 257 98 0.5 - 188.2 (31.1)
6P LOSS MUTATED 60 14 4.4 - 188.2 (37.3)
6P LOSS WILD-TYPE 197 84 0.5 - 171.1 (29.0)

Figure S98.  Get High-res Image Gene #52: '6p loss' versus Clinical Feature #1: 'Time to Death'

'8q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0399 (Wilcoxon-test), Q value = 0.24

Table S99.  Gene #57: '8q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
8Q LOSS MUTATED 45 65.0 (13.1)
8Q LOSS WILD-TYPE 211 59.9 (15.0)

Figure S99.  Get High-res Image Gene #57: '8q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'9p loss' versus 'YEARS_TO_BIRTH'

P value = 0.00215 (Wilcoxon-test), Q value = 0.054

Table S100.  Gene #58: '9p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
9P LOSS MUTATED 82 65.0 (13.5)
9P LOSS WILD-TYPE 174 58.9 (14.9)

Figure S100.  Get High-res Image Gene #58: '9p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'9q loss' versus 'Time to Death'

P value = 0.0375 (logrank test), Q value = 0.23

Table S101.  Gene #59: '9q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 257 98 0.5 - 188.2 (31.1)
9Q LOSS MUTATED 50 25 0.6 - 188.2 (20.2)
9Q LOSS WILD-TYPE 207 73 0.5 - 159.3 (33.3)

Figure S101.  Get High-res Image Gene #59: '9q loss' versus Clinical Feature #1: 'Time to Death'

'10p loss' versus 'YEARS_TO_BIRTH'

P value = 0.0116 (Wilcoxon-test), Q value = 0.12

Table S102.  Gene #60: '10p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
10P LOSS MUTATED 121 63.3 (14.4)
10P LOSS WILD-TYPE 135 58.7 (14.7)

Figure S102.  Get High-res Image Gene #60: '10p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'10p loss' versus 'GENDER'

P value = 0.00406 (Fisher's exact test), Q value = 0.07

Table S103.  Gene #60: '10p loss' versus Clinical Feature #4: 'GENDER'

nPatients FEMALE MALE
ALL 139 118
10P LOSS MUTATED 77 44
10P LOSS WILD-TYPE 62 74

Figure S103.  Get High-res Image Gene #60: '10p loss' versus Clinical Feature #4: 'GENDER'

'10p loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00092

Table S104.  Gene #60: '10p loss' 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
10P LOSS MUTATED 12 0 0 61 7 13 14 0 0 1 13
10P LOSS WILD-TYPE 47 2 1 42 2 11 14 2 2 5 8

Figure S104.  Get High-res Image Gene #60: '10p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'10q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0108 (Wilcoxon-test), Q value = 0.12

Table S105.  Gene #61: '10q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
10Q LOSS MUTATED 131 63.4 (13.3)
10Q LOSS WILD-TYPE 125 58.2 (15.7)

Figure S105.  Get High-res Image Gene #61: '10q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'10q loss' versus 'GENDER'

P value = 0.00597 (Fisher's exact test), Q value = 0.092

Table S106.  Gene #61: '10q loss' versus Clinical Feature #4: 'GENDER'

nPatients FEMALE MALE
ALL 139 118
10Q LOSS MUTATED 82 49
10Q LOSS WILD-TYPE 57 69

Figure S106.  Get High-res Image Gene #61: '10q loss' versus Clinical Feature #4: 'GENDER'

'10q loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00092

Table S107.  Gene #61: '10q loss' 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
10Q LOSS MUTATED 8 0 0 75 4 14 15 0 0 0 15
10Q LOSS WILD-TYPE 51 2 1 28 5 10 13 2 2 6 6

Figure S107.  Get High-res Image Gene #61: '10q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'11q loss' versus 'RADIATION_THERAPY'

P value = 0.0206 (Fisher's exact test), Q value = 0.17

Table S108.  Gene #63: '11q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 179 72
11Q LOSS MUTATED 58 35
11Q LOSS WILD-TYPE 121 37

Figure S108.  Get High-res Image Gene #63: '11q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'13q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0013 (Wilcoxon-test), Q value = 0.038

Table S109.  Gene #66: '13q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
13Q LOSS MUTATED 132 63.7 (14.0)
13Q LOSS WILD-TYPE 124 57.8 (14.9)

Figure S109.  Get High-res Image Gene #66: '13q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'13q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.016 (Fisher's exact test), Q value = 0.15

Table S110.  Gene #66: '13q loss' 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
13Q LOSS MUTATED 22 0 0 58 6 13 18 0 0 1 14
13Q LOSS WILD-TYPE 37 2 1 45 3 11 10 2 2 5 7

Figure S110.  Get High-res Image Gene #66: '13q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'15q loss' versus 'Time to Death'

P value = 0.000728 (logrank test), Q value = 0.027

Table S111.  Gene #68: '15q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 257 98 0.5 - 188.2 (31.1)
15Q LOSS MUTATED 46 26 3.1 - 171.1 (20.8)
15Q LOSS WILD-TYPE 211 72 0.5 - 188.2 (33.3)

Figure S111.  Get High-res Image Gene #68: '15q loss' versus Clinical Feature #1: 'Time to Death'

'15q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0186 (Wilcoxon-test), Q value = 0.16

Table S112.  Gene #68: '15q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
15Q LOSS MUTATED 46 65.5 (13.3)
15Q LOSS WILD-TYPE 210 59.8 (14.9)

Figure S112.  Get High-res Image Gene #68: '15q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'16p loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00092

Table S113.  Gene #69: '16p loss' 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
16P LOSS MUTATED 8 0 0 32 2 5 11 0 0 0 17
16P LOSS WILD-TYPE 51 2 1 71 7 19 17 2 2 6 4

Figure S113.  Get High-res Image Gene #69: '16p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'16q loss' versus 'YEARS_TO_BIRTH'

P value = 0.00214 (Wilcoxon-test), Q value = 0.054

Table S114.  Gene #70: '16q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
16Q LOSS MUTATED 123 63.6 (13.7)
16Q LOSS WILD-TYPE 133 58.3 (15.3)

Figure S114.  Get High-res Image Gene #70: '16q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'16q loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00092

Table S115.  Gene #70: '16q loss' 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
16Q LOSS MUTATED 14 0 0 65 2 9 16 0 1 0 17
16Q LOSS WILD-TYPE 45 2 1 38 7 15 12 2 1 6 4

Figure S115.  Get High-res Image Gene #70: '16q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'17q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0251 (Wilcoxon-test), Q value = 0.18

Table S116.  Gene #72: '17q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
17Q LOSS MUTATED 49 64.2 (16.0)
17Q LOSS WILD-TYPE 207 60.0 (14.4)

Figure S116.  Get High-res Image Gene #72: '17q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'17q loss' versus 'RADIATION_THERAPY'

P value = 0.00385 (Fisher's exact test), Q value = 0.07

Table S117.  Gene #72: '17q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 179 72
17Q LOSS MUTATED 25 22
17Q LOSS WILD-TYPE 154 50

Figure S117.  Get High-res Image Gene #72: '17q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'19p loss' versus 'RADIATION_THERAPY'

P value = 0.0299 (Fisher's exact test), Q value = 0.2

Table S118.  Gene #75: '19p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 179 72
19P LOSS MUTATED 12 12
19P LOSS WILD-TYPE 167 60

Figure S118.  Get High-res Image Gene #75: '19p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'20p loss' versus 'YEARS_TO_BIRTH'

P value = 0.0032 (Wilcoxon-test), Q value = 0.069

Table S119.  Gene #77: '20p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
20P LOSS MUTATED 55 65.7 (11.6)
20P LOSS WILD-TYPE 201 59.5 (15.2)

Figure S119.  Get High-res Image Gene #77: '20p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'20p loss' versus 'RADIATION_THERAPY'

P value = 0.0184 (Fisher's exact test), Q value = 0.16

Table S120.  Gene #77: '20p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 179 72
20P LOSS MUTATED 32 23
20P LOSS WILD-TYPE 147 49

Figure S120.  Get High-res Image Gene #77: '20p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'20q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0209 (Wilcoxon-test), Q value = 0.17

Table S121.  Gene #78: '20q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
20Q LOSS MUTATED 25 67.4 (10.6)
20Q LOSS WILD-TYPE 231 60.1 (15.0)

Figure S121.  Get High-res Image Gene #78: '20q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'20q loss' versus 'RESIDUAL_TUMOR'

P value = 0.0348 (Fisher's exact test), Q value = 0.22

Table S122.  Gene #78: '20q loss' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 152 69 9 26
20Q LOSS MUTATED 21 3 1 0
20Q LOSS WILD-TYPE 131 66 8 26

Figure S122.  Get High-res Image Gene #78: '20q loss' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'21q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0277 (Wilcoxon-test), Q value = 0.2

Table S123.  Gene #79: '21q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 256 60.8 (14.7)
21Q LOSS MUTATED 50 65.1 (11.9)
21Q LOSS WILD-TYPE 206 59.8 (15.2)

Figure S123.  Get High-res Image Gene #79: '21q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'22q loss' versus 'GENDER'

P value = 0.0324 (Fisher's exact test), Q value = 0.21

Table S124.  Gene #80: '22q loss' versus Clinical Feature #4: 'GENDER'

nPatients FEMALE MALE
ALL 139 118
22Q LOSS MUTATED 44 23
22Q LOSS WILD-TYPE 95 95

Figure S124.  Get High-res Image Gene #80: '22q loss' versus Clinical Feature #4: 'GENDER'

'xq loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00017 (Fisher's exact test), Q value = 0.0088

Table S125.  Gene #82: 'xq loss' 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
XQ LOSS MUTATED 13 0 0 57 5 4 12 0 0 1 10
XQ LOSS WILD-TYPE 46 2 1 46 4 20 16 2 2 5 11

Figure S125.  Get High-res Image Gene #82: 'xq loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

Methods & Data
Input

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

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/SARC-TP/22534095/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 arm-level cnvs = 82

  • Number of selected clinical features = 9

  • Exclude regions that fewer than K tumors have mutations, K = 3

Survival analysis

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

Fisher's exact test

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

Q value calculation

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

Download Results

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

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