Correlation between copy number variations of arm-level result and selected clinical features

Sarcoma (Primary solid tumor)

21 August 2015 | analyses__2015_08_21

Maintainer Information

Citation Information

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

Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1542MWV

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 256 patients, 128 significant findings detected with Q value < 0.25.

1p gain cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', 'HISTOLOGICAL_TYPE', and 'RACE'.
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', 'TUMOR_TISSUE_SITE', 'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.
8p gain cnv correlated to 'Time to Death', 'HISTOLOGICAL_TYPE', 'RESIDUAL_TUMOR', 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', 'HISTOLOGICAL_TYPE', and 'RACE'.
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'.
15q gain cnv correlated to 'YEARS_TO_BIRTH'.
16p gain cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', and 'HISTOLOGICAL_TYPE'.
17p gain cnv correlated to 'YEARS_TO_BIRTH'.
17q gain cnv correlated to 'HISTOLOGICAL_TYPE'.
18p gain cnv correlated to 'YEARS_TO_BIRTH', 'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.
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' and 'RADIATION_THERAPY'.
xp gain cnv correlated to 'HISTOLOGICAL_TYPE'.
xq gain cnv correlated to 'ETHNICITY'.
1p loss cnv correlated to 'GENDER'.
1q loss cnv correlated to 'RADIATION_THERAPY'.
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 'RADIATION_THERAPY'.
4q loss cnv correlated to 'RADIATION_THERAPY'.
6p loss cnv correlated to 'Time to Death'.
8q loss cnv correlated to 'YEARS_TO_BIRTH'.
9p loss cnv correlated to 'YEARS_TO_BIRTH'.
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'.
18q loss cnv correlated to 'Time to Death', 'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.
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'.
21q loss cnv correlated to 'YEARS_TO_BIRTH'.
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, 128 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	56 (22%)	200	0.00211 (0.0503)	0.0234 (0.171)	0.00852 (0.101)	0.452 (0.791)	0.0105 (0.116)	0.027 (0.188)	0.402 (0.752)	0.0361 (0.22)	0.589 (0.857)
5p gain	98 (38%)	158	0.764 (0.968)	0.000581 (0.0198)	0.00419 (0.0717)	0.607 (0.87)	0.00349 (0.0695)	0.0025 (0.0559)	0.656 (0.908)	0.771 (0.968)	1 (1.00)
7p gain	82 (32%)	174	0.421 (0.77)	7.54e-06 (0.00105)	0.0237 (0.172)	1 (1.00)	0.0151 (0.134)	1e-05 (0.00105)	0.877 (1.00)	0.455 (0.791)	0.656 (0.908)
7q gain	68 (27%)	188	0.189 (0.518)	4.83e-07 (0.000356)	0.00808 (0.1)	0.118 (0.41)	0.00387 (0.0696)	0.00059 (0.0198)	0.441 (0.791)	0.794 (0.981)	0.13 (0.428)
8p gain	52 (20%)	204	0.00799 (0.1)	0.0771 (0.36)	0.265 (0.626)	1 (1.00)	0.0784 (0.36)	0.0153 (0.134)	0.0388 (0.227)	0.0295 (0.199)	0.29 (0.662)
12p gain	43 (17%)	213	0.00491 (0.0771)	0.000179 (0.00879)	0.0745 (0.357)	0.738 (0.963)	0.137 (0.44)	0.00037 (0.0148)	0.685 (0.926)	0.0383 (0.226)	0.182 (0.511)
20q gain	83 (32%)	173	0.00452 (0.0727)	0.000237 (0.0109)	0.174 (0.497)	0.0076 (0.1)	0.172 (0.497)	0.00695 (0.0933)	0.28 (0.646)	0.663 (0.908)	1 (1.00)
6p gain	51 (20%)	205	0.000103 (0.0061)	0.0123 (0.125)	0.863 (1.00)	0.274 (0.638)	0.159 (0.474)	0.0319 (0.207)	0.817 (0.996)	0.56 (0.857)	1 (1.00)
9q gain	73 (29%)	183	0.919 (1.00)	7.38e-06 (0.00105)	0.012 (0.125)	0.333 (0.708)	0.535 (0.841)	5e-05 (0.00335)	0.346 (0.711)	0.683 (0.926)	1 (1.00)
11p gain	23 (9%)	233	0.00534 (0.0821)	4.57e-05 (0.00335)	0.649 (0.905)	0.662 (0.908)	0.21 (0.554)	0.0183 (0.153)	0.249 (0.608)	0.261 (0.622)	1 (1.00)
12q gain	34 (13%)	222	0.394 (0.747)	0.138 (0.44)	0.0449 (0.254)	0.0633 (0.316)	0.0373 (0.224)	1e-05 (0.00105)	0.747 (0.965)	0.0121 (0.125)	0.125 (0.424)
14q gain	57 (22%)	199	0.0233 (0.171)	0.0063 (0.0894)	0.0088 (0.103)	0.765 (0.968)	0.0925 (0.375)	0.0773 (0.36)	0.874 (1.00)	0.829 (1.00)	1 (1.00)
16p gain	40 (16%)	216	0.0155 (0.134)	0.0142 (0.131)	0.739 (0.963)	0.606 (0.87)	0.255 (0.613)	0.025 (0.179)	0.669 (0.915)	0.488 (0.804)	1 (1.00)
18p gain	53 (21%)	203	0.15 (0.46)	0.0127 (0.126)	0.694 (0.929)	0.355 (0.719)	0.00152 (0.043)	0.023 (0.171)	0.973 (1.00)	0.381 (0.733)	0.586 (0.857)
2p loss	88 (34%)	168	0.299 (0.672)	0.00571 (0.0839)	0.453 (0.791)	0.188 (0.515)	0.135 (0.439)	0.0058 (0.0839)	0.643 (0.9)	0.0322 (0.207)	0.164 (0.481)
10p loss	120 (47%)	136	0.738 (0.963)	0.0184 (0.153)	0.353 (0.717)	0.00821 (0.1)	0.0488 (0.269)	2e-05 (0.00164)	0.705 (0.936)	0.116 (0.409)	0.372 (0.728)
10q loss	131 (51%)	125	0.304 (0.678)	0.0101 (0.115)	0.247 (0.607)	0.00831 (0.1)	0.0911 (0.374)	1e-05 (0.00105)	0.937 (1.00)	0.127 (0.424)	0.19 (0.519)
18q loss	72 (28%)	184	0.0297 (0.199)	0.0801 (0.36)	0.181 (0.51)	1 (1.00)	0.0279 (0.192)	0.0193 (0.156)	0.692 (0.929)	1 (1.00)	1 (1.00)
3p gain	39 (15%)	217	0.978 (1.00)	0.0752 (0.358)	0.0225 (0.171)	0.384 (0.735)	0.331 (0.706)	0.00068 (0.0218)	0.987 (1.00)	0.0514 (0.279)	1 (1.00)
3q gain	36 (14%)	220	0.655 (0.908)	0.0306 (0.203)	0.0879 (0.368)	0.471 (0.801)	0.221 (0.566)	0.00379 (0.0696)	0.785 (0.976)	0.101 (0.397)	1 (1.00)
4p gain	68 (27%)	188	0.0606 (0.308)	0.774 (0.968)	0.109 (0.406)	0.398 (0.752)	0.342 (0.71)	0.00204 (0.0502)	0.0377 (0.225)	0.855 (1.00)	1 (1.00)
5q gain	71 (28%)	185	0.347 (0.711)	0.013 (0.126)	0.0081 (0.1)	0.575 (0.857)	0.0849 (0.364)	0.432 (0.787)	0.343 (0.71)	0.305 (0.678)	1 (1.00)
9p gain	57 (22%)	199	0.0871 (0.368)	0.00121 (0.0357)	0.399 (0.752)	0.174 (0.497)	0.501 (0.811)	0.0122 (0.125)	0.744 (0.965)	0.414 (0.768)	1 (1.00)
11q gain	22 (9%)	234	0.00399 (0.0701)	0.0137 (0.128)	0.759 (0.968)	0.662 (0.908)	0.0776 (0.36)	0.105 (0.4)	0.446 (0.791)	0.524 (0.832)	1 (1.00)
19p gain	87 (34%)	169	0.0847 (0.364)	0.000107 (0.0061)	0.442 (0.791)	0.113 (0.408)	0.46 (0.791)	0.00453 (0.0727)	0.246 (0.606)	0.932 (1.00)	0.341 (0.71)
19q gain	65 (25%)	191	0.472 (0.801)	0.00428 (0.0717)	0.53 (0.837)	0.15 (0.46)	0.0519 (0.279)	0.00679 (0.0933)	0.788 (0.977)	0.854 (1.00)	1 (1.00)
20p gain	62 (24%)	194	0.000481 (0.0178)	0.0111 (0.118)	0.836 (1.00)	0.0577 (0.3)	0.624 (0.881)	0.401 (0.752)	0.504 (0.812)	0.355 (0.719)	1 (1.00)
21q gain	58 (23%)	198	0.0181 (0.153)	0.0198 (0.157)	0.082 (0.36)	0.299 (0.672)	0.865 (1.00)	0.115 (0.409)	0.361 (0.721)	0.0482 (0.267)	0.592 (0.857)
22q gain	60 (23%)	196	0.485 (0.804)	0.00163 (0.0431)	0.456 (0.791)	0.554 (0.856)	0.0311 (0.203)	0.0872 (0.368)	0.453 (0.791)	0.915 (1.00)	0.0954 (0.381)
2q loss	71 (28%)	185	0.000721 (0.0222)	0.000297 (0.0129)	0.139 (0.44)	0.487 (0.804)	0.113 (0.408)	0.0877 (0.368)	0.691 (0.929)	0.0907 (0.374)	0.325 (0.699)
3p loss	56 (22%)	200	0.156 (0.471)	0.013 (0.126)	0.155 (0.469)	0.762 (0.968)	0.125 (0.424)	0.00567 (0.0839)	0.213 (0.56)	0.911 (1.00)	1 (1.00)
3q loss	49 (19%)	207	0.0361 (0.22)	0.00939 (0.108)	0.49 (0.804)	0.154 (0.467)	0.107 (0.404)	0.219 (0.564)	0.113 (0.408)	0.816 (0.996)	1 (1.00)
13q loss	132 (52%)	124	0.486 (0.804)	0.00174 (0.0442)	0.787 (0.977)	0.0789 (0.36)	0.321 (0.699)	0.0149 (0.134)	0.441 (0.791)	1 (1.00)	0.671 (0.915)
15q loss	45 (18%)	211	0.000172 (0.00879)	0.0194 (0.156)	0.0924 (0.375)	0.51 (0.818)	0.362 (0.721)	0.692 (0.929)	0.856 (1.00)	0.284 (0.654)	0.589 (0.857)
16q loss	124 (48%)	132	0.216 (0.564)	0.00278 (0.059)	0.0563 (0.295)	0.104 (0.4)	0.48 (0.804)	1e-05 (0.00105)	0.36 (0.721)	0.0805 (0.36)	1 (1.00)
17q loss	48 (19%)	208	0.111 (0.407)	0.0268 (0.188)	0.552 (0.856)	0.339 (0.71)	0.0107 (0.116)	0.344 (0.71)	0.723 (0.953)	0.294 (0.666)	0.587 (0.857)
20p loss	55 (21%)	201	0.302 (0.676)	0.00363 (0.0696)	0.0772 (0.36)	0.363 (0.721)	0.0105 (0.116)	0.196 (0.532)	0.0645 (0.32)	0.589 (0.857)	1 (1.00)
2p gain	22 (9%)	234	0.467 (0.797)	0.266 (0.626)	0.418 (0.77)	0.662 (0.908)	0.626 (0.881)	0.0206 (0.161)	0.109 (0.406)	0.65 (0.905)	0.375 (0.728)
2q gain	22 (9%)	234	0.439 (0.791)	0.363 (0.721)	0.745 (0.965)	0.187 (0.515)	0.626 (0.881)	0.00288 (0.059)	0.608 (0.87)	0.536 (0.841)	0.375 (0.728)
4q gain	47 (18%)	209	0.109 (0.406)	0.551 (0.855)	0.59 (0.857)	0.631 (0.885)	0.274 (0.638)	0.00695 (0.0933)	0.541 (0.845)	1 (1.00)	1 (1.00)
6q gain	50 (20%)	206	0.0154 (0.134)	0.0521 (0.279)	0.95 (1.00)	0.115 (0.409)	0.153 (0.467)	0.237 (0.59)	0.754 (0.968)	0.562 (0.857)	1 (1.00)
8q gain	65 (25%)	191	0.0132 (0.127)	0.367 (0.722)	0.0809 (0.36)	0.473 (0.801)	0.419 (0.77)	0.0742 (0.357)	0.488 (0.804)	0.0613 (0.308)	0.114 (0.409)
10p gain	23 (9%)	233	0.227 (0.574)	0.679 (0.925)	0.577 (0.857)	0.662 (0.908)	1 (1.00)	0.0288 (0.197)	0.345 (0.71)	0.805 (0.988)	1 (1.00)
10q gain	12 (5%)	244	0.522 (0.83)	0.761 (0.968)	0.693 (0.929)	0.775 (0.968)	0.519 (0.828)	0.0417 (0.242)	0.24 (0.596)	1 (1.00)	1 (1.00)
13q gain	15 (6%)	241	0.597 (0.861)	0.629 (0.884)	0.558 (0.857)	0.0589 (0.304)	0.567 (0.857)	0.0824 (0.36)	0.406 (0.759)	0.023 (0.171)	1 (1.00)
15q gain	63 (25%)	193	0.685 (0.926)	0.0349 (0.218)	0.41 (0.764)	0.109 (0.406)	0.326 (0.699)	0.462 (0.791)	0.803 (0.988)	0.657 (0.908)	0.105 (0.4)
17p gain	61 (24%)	195	0.0815 (0.36)	0.0351 (0.218)	0.839 (1.00)	0.77 (0.968)	0.185 (0.513)	0.044 (0.252)	0.0882 (0.368)	0.225 (0.572)	1 (1.00)
17q gain	57 (22%)	199	0.78 (0.972)	0.184 (0.513)	0.452 (0.791)	0.0724 (0.351)	0.232 (0.582)	0.00288 (0.059)	0.265 (0.626)	0.143 (0.447)	0.596 (0.861)
18q gain	36 (14%)	220	0.225 (0.572)	0.0262 (0.186)	0.578 (0.857)	0.279 (0.645)	1 (1.00)	0.444 (0.791)	0.292 (0.663)	0.38 (0.733)	1 (1.00)
xp gain	74 (29%)	182	0.326 (0.699)	0.0563 (0.295)	0.204 (0.543)	0.072 (0.351)	0.437 (0.791)	0.0428 (0.247)	0.362 (0.721)	0.865 (1.00)	0.176 (0.497)
xq gain	33 (13%)	223	0.519 (0.828)	0.391 (0.746)	0.369 (0.724)	0.461 (0.791)	0.296 (0.667)	0.127 (0.424)	0.215 (0.562)	1 (1.00)	0.0162 (0.139)
1p loss	32 (12%)	224	0.061 (0.308)	0.251 (0.609)	0.385 (0.735)	0.0135 (0.127)	1 (1.00)	0.35 (0.716)	0.489 (0.804)	0.289 (0.662)	1 (1.00)
1q loss	40 (16%)	216	0.96 (1.00)	0.252 (0.609)	0.905 (1.00)	0.491 (0.804)	0.0328 (0.208)	0.0993 (0.392)	0.907 (1.00)	0.708 (0.938)	0.563 (0.857)
4p loss	42 (16%)	214	0.545 (0.851)	0.0836 (0.363)	0.818 (0.996)	0.501 (0.811)	0.0207 (0.161)	0.413 (0.768)	0.144 (0.449)	0.315 (0.693)	1 (1.00)
4q loss	51 (20%)	205	0.754 (0.968)	0.122 (0.421)	0.734 (0.963)	0.116 (0.409)	0.0348 (0.218)	0.418 (0.77)	0.505 (0.812)	0.497 (0.809)	0.586 (0.857)
6p loss	60 (23%)	196	0.00159 (0.0431)	0.935 (1.00)	0.905 (1.00)	0.375 (0.728)	0.868 (1.00)	0.314 (0.692)	0.579 (0.857)	0.704 (0.936)	1 (1.00)
8q loss	46 (18%)	210	0.761 (0.968)	0.0367 (0.222)	0.838 (1.00)	0.624 (0.881)	0.202 (0.541)	0.451 (0.791)	0.923 (1.00)	0.147 (0.454)	0.587 (0.857)
9p loss	83 (32%)	173	0.259 (0.619)	0.00249 (0.0559)	0.117 (0.409)	0.228 (0.574)	0.453 (0.791)	0.578 (0.857)	0.0953 (0.381)	0.451 (0.791)	1 (1.00)
11q loss	91 (36%)	165	0.278 (0.645)	0.73 (0.96)	0.881 (1.00)	0.896 (1.00)	0.0192 (0.156)	0.172 (0.497)	0.529 (0.837)	0.769 (0.968)	0.166 (0.486)
16p loss	75 (29%)	181	0.338 (0.71)	0.184 (0.513)	0.501 (0.811)	0.169 (0.49)	0.437 (0.791)	2e-05 (0.00164)	0.884 (1.00)	0.135 (0.439)	1 (1.00)
19p loss	21 (8%)	235	0.575 (0.857)	0.536 (0.841)	0.46 (0.791)	0.823 (0.999)	0.0037 (0.0696)	0.31 (0.686)	0.0461 (0.258)	0.243 (0.6)	1 (1.00)
20q loss	25 (10%)	231	0.749 (0.965)	0.0224 (0.171)	0.128 (0.424)	0.399 (0.752)	0.161 (0.476)	0.367 (0.722)	0.0818 (0.36)	0.837 (1.00)	1 (1.00)
21q loss	50 (20%)	206	0.252 (0.609)	0.031 (0.203)	0.962 (1.00)	1 (1.00)	0.291 (0.662)	0.0502 (0.274)	0.219 (0.564)	0.906 (1.00)	1 (1.00)
xq loss	101 (39%)	155	0.141 (0.444)	0.59 (0.857)	0.34 (0.71)	0.125 (0.424)	0.886 (1.00)	0.00038 (0.0148)	0.774 (0.968)	0.353 (0.717)	0.159 (0.474)
1q gain	49 (19%)	207	0.798 (0.983)	0.102 (0.397)	0.342 (0.71)	0.11 (0.407)	0.858 (1.00)	0.0703 (0.346)	0.913 (1.00)	0.9 (1.00)	0.586 (0.857)
16q gain	21 (8%)	235	0.48 (0.804)	0.948 (1.00)	0.852 (1.00)	0.502 (0.811)	0.127 (0.424)	0.622 (0.881)	0.741 (0.964)	1 (1.00)	1 (1.00)
5p loss	22 (9%)	234	0.325 (0.699)	0.772 (0.968)	0.458 (0.791)	0.187 (0.515)	1 (1.00)	0.145 (0.449)	0.0598 (0.306)	0.229 (0.574)	1 (1.00)
5q loss	35 (14%)	221	0.263 (0.625)	0.113 (0.408)	0.478 (0.804)	0.584 (0.857)	0.684 (0.926)	0.272 (0.638)	0.133 (0.435)	0.583 (0.857)	1 (1.00)
6q loss	53 (21%)	203	0.219 (0.564)	0.815 (0.996)	0.774 (0.968)	0.217 (0.564)	0.225 (0.572)	0.0992 (0.392)	0.737 (0.963)	1 (1.00)	1 (1.00)
7p loss	32 (12%)	224	0.702 (0.935)	0.365 (0.722)	0.867 (1.00)	0.129 (0.425)	0.833 (1.00)	0.721 (0.952)	0.588 (0.857)	0.175 (0.497)	1 (1.00)
7q loss	34 (13%)	222	0.137 (0.44)	0.42 (0.77)	0.853 (1.00)	0.712 (0.942)	0.835 (1.00)	0.901 (1.00)	0.861 (1.00)	1 (1.00)	1 (1.00)
8p loss	62 (24%)	194	0.202 (0.541)	0.339 (0.71)	0.577 (0.857)	0.77 (0.968)	1 (1.00)	0.916 (1.00)	0.817 (0.996)	0.126 (0.424)	0.591 (0.857)
9q loss	51 (20%)	205	0.0563 (0.295)	0.0937 (0.378)	0.843 (1.00)	0.531 (0.837)	0.481 (0.804)	0.65 (0.905)	0.21 (0.554)	0.14 (0.443)	1 (1.00)
11p loss	94 (37%)	162	0.695 (0.929)	0.208 (0.551)	0.793 (0.981)	0.897 (1.00)	0.0795 (0.36)	0.857 (1.00)	0.467 (0.797)	0.935 (1.00)	0.16 (0.474)
12p loss	65 (25%)	191	0.564 (0.857)	0.125 (0.424)	0.881 (1.00)	0.565 (0.857)	0.872 (1.00)	0.0898 (0.372)	0.878 (1.00)	0.176 (0.497)	0.33 (0.705)
12q loss	54 (21%)	202	0.768 (0.968)	0.251 (0.609)	0.699 (0.933)	0.445 (0.791)	0.487 (0.804)	0.62 (0.881)	0.82 (0.997)	0.273 (0.638)	0.587 (0.857)
14q loss	62 (24%)	194	0.199 (0.536)	0.61 (0.871)	0.548 (0.854)	1 (1.00)	1 (1.00)	0.875 (1.00)	0.429 (0.784)	0.393 (0.747)	0.592 (0.857)
17p loss	57 (22%)	199	0.318 (0.694)	0.104 (0.4)	0.608 (0.87)	1 (1.00)	0.166 (0.486)	0.381 (0.733)	0.919 (1.00)	0.441 (0.791)	1 (1.00)
18p loss	62 (24%)	194	0.137 (0.44)	0.361 (0.721)	0.866 (1.00)	1 (1.00)	0.326 (0.699)	0.625 (0.881)	0.969 (1.00)	0.919 (1.00)	1 (1.00)
19q loss	39 (15%)	217	0.742 (0.964)	0.798 (0.983)	0.944 (1.00)	0.862 (1.00)	0.243 (0.6)	0.491 (0.804)	0.455 (0.791)	0.486 (0.804)	0.199 (0.536)
22q loss	66 (26%)	190	0.939 (1.00)	0.138 (0.44)	0.461 (0.791)	0.0451 (0.254)	0.749 (0.965)	0.312 (0.689)	0.494 (0.807)	1 (1.00)	0.341 (0.71)
xp loss	62 (24%)	194	0.984 (1.00)	0.158 (0.474)	0.555 (0.856)	0.38 (0.733)	0.512 (0.82)	0.105 (0.4)	0.866 (1.00)	0.317 (0.694)	0.589 (0.857)

'1p gain' versus 'Time to Death'

P value = 0.00211 (logrank test), Q value = 0.05

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

	nPatients	nDeath	Duration Range (Median), Month
ALL	256	94	0.5 - 188.2 (26.4)
1P GAIN MUTATED	56	28	1.1 - 106.5 (22.3)
1P GAIN WILD-TYPE	200	66	0.5 - 188.2 (30.2)

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 = 0.0234 (Wilcoxon-test), Q value = 0.17

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

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
1P GAIN MUTATED	56	64.6 (13.7)
1P GAIN WILD-TYPE	199	59.9 (14.8)

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 = 0.00852 (Fisher's exact test), Q value = 0.1

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	43	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	5	0	1	0	1	0	1	2
1P GAIN WILD-TYPE	1	5	1	1	2	1	20	1	1	2	1	1	9	2	4	1	10	3	26	4	1	5	6	1	0	68	3	1	5	3	1	6	3

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

'1p gain' versus 'RADIATION_THERAPY'

P value = 0.0105 (Fisher's exact test), Q value = 0.12

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

nPatients	NO	YES
ALL	180	69
1P GAIN MUTATED	32	23
1P GAIN WILD-TYPE	148	46

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

'1p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.027 (Fisher's exact test), Q value = 0.19

Table S5. 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	23	28	2	2	6	21
1P GAIN MUTATED	5	0	0	24	1	7	11	1	0	0	7
1P GAIN WILD-TYPE	54	2	1	79	8	16	17	1	2	6	14

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

'1p gain' versus 'RACE'

P value = 0.0361 (Fisher's exact test), Q value = 0.22

Table S6. Gene #1: '1p gain' versus Clinical Feature #8: 'RACE'

nPatients	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	6	18	223
1P GAIN MUTATED	0	8	45
1P GAIN WILD-TYPE	6	10	178

Figure S6. Get High-res Image Gene #1: '1p gain' versus Clinical Feature #8: 'RACE'

'2p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0206 (Fisher's exact test), Q value = 0.16

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	23	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	21	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 = 0.00288 (Fisher's exact test), Q value = 0.059

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	23	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	20	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 = 0.0225 (Fisher's exact test), Q value = 0.17

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	43	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	4	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	27	3	1	5	8	2	1	69	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 = 0.00068 (Fisher's exact test), Q value = 0.022

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	23	28	2	2	6	21
3P GAIN MUTATED	1	0	0	18	0	3	11	0	0	0	6
3P GAIN WILD-TYPE	58	2	1	85	9	20	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 = 0.0306 (Wilcoxon-test), Q value = 0.2

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

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
3Q GAIN MUTATED	36	65.8 (13.4)
3Q GAIN WILD-TYPE	219	60.1 (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 = 0.00379 (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	23	28	2	2	6	21
3Q GAIN MUTATED	1	0	0	16	0	4	10	0	0	0	5
3Q GAIN WILD-TYPE	58	2	1	87	9	19	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 = 0.00204 (Fisher's exact test), Q value = 0.05

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	23	28	2	2	6	21
4P GAIN MUTATED	9	0	0	23	4	8	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 = 0.0377 (Fisher's exact test), Q value = 0.22

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

nPatients	R0	R1	R2	RX
ALL	152	68	9	26
4P GAIN MUTATED	36	17	1	13
4P GAIN WILD-TYPE	116	51	8	13

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

'4q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00695 (Fisher's exact test), Q value = 0.093

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	23	28	2	2	6	21
4Q GAIN MUTATED	6	0	0	16	2	3	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 = 0.000581 (Wilcoxon-test), Q value = 0.02

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

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
5P GAIN MUTATED	97	65.1 (12.8)
5P GAIN WILD-TYPE	158	58.4 (15.2)

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 = 0.00419 (Fisher's exact test), Q value = 0.072

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	43	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	7	4	24	0	1	1	3	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	10	1	19	4	1	4	5	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 = 0.00349 (Fisher's exact test), Q value = 0.07

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

nPatients	NO	YES
ALL	180	69
5P GAIN MUTATED	59	37
5P GAIN WILD-TYPE	121	32

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

'5p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0025 (Fisher's exact test), Q value = 0.056

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	23	28	2	2	6	21
5P GAIN MUTATED	15	0	0	39	3	10	18	0	0	0	13
5P GAIN WILD-TYPE	44	2	1	64	6	13	10	2	2	6	8

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

'5q gain' versus 'YEARS_TO_BIRTH'

P value = 0.013 (Wilcoxon-test), Q value = 0.13

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

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
5Q GAIN MUTATED	71	64.8 (13.4)
5Q GAIN WILD-TYPE	184	59.5 (14.9)

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 = 0.0081 (Fisher's exact test), Q value = 0.1

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	43	4	2	5	8	2	1	73	3	2	5	4	1	7	5
5Q GAIN MUTATED	0	1	0	0	0	0	6	2	0	1	0	2	1	1	0	0	3	4	18	0	1	1	3	1	1	16	0	0	1	1	0	6	1
5Q GAIN WILD-TYPE	1	6	2	1	2	1	22	0	1	1	1	0	9	1	4	2	14	1	25	4	1	4	5	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 = 0.000103 (logrank test), Q value = 0.0061

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

	nPatients	nDeath	Duration Range (Median), Month
ALL	256	94	0.5 - 188.2 (26.4)
6P GAIN MUTATED	51	29	0.6 - 143.4 (22.6)
6P GAIN WILD-TYPE	205	65	0.5 - 188.2 (27.8)

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 = 0.0123 (Wilcoxon-test), Q value = 0.12

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

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
6P GAIN MUTATED	50	65.8 (13.1)
6P GAIN WILD-TYPE	205	59.8 (14.8)

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

'6p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0319 (Fisher's exact test), Q value = 0.21

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	23	28	2	2	6	21
6P GAIN MUTATED	11	0	0	15	0	8	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 = 0.0154 (logrank test), Q value = 0.13

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

	nPatients	nDeath	Duration Range (Median), Month
ALL	256	94	0.5 - 188.2 (26.4)
6Q GAIN MUTATED	50	24	0.6 - 143.4 (26.8)
6Q GAIN WILD-TYPE	206	70	0.5 - 188.2 (26.4)

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 = 7.54e-06 (Wilcoxon-test), Q value = 0.0011

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

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
7P GAIN MUTATED	81	66.6 (12.7)
7P GAIN WILD-TYPE	174	58.3 (14.8)

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 = 0.0237 (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	43	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	27	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 = 0.0151 (Fisher's exact test), Q value = 0.13

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

nPatients	NO	YES
ALL	180	69
7P GAIN MUTATED	50	31
7P GAIN WILD-TYPE	130	38

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 = 0.0011

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	23	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	10	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 = 4.83e-07 (Wilcoxon-test), Q value = 0.00036

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

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
7Q GAIN MUTATED	68	68.4 (10.7)
7Q GAIN WILD-TYPE	187	58.2 (15.0)

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

'7q gain' versus 'TUMOR_TISSUE_SITE'

P value = 0.00808 (Fisher's exact test), Q value = 0.1

Table S31. Gene #14: '7q 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	43	4	2	5	8	2	1	73	3	2	5	4	1	7	5
7Q GAIN MUTATED	0	3	0	0	0	1	2	1	0	0	0	1	4	0	0	0	8	0	16	1	0	1	1	0	0	14	0	1	3	3	0	5	3
7Q GAIN WILD-TYPE	1	4	2	1	2	0	26	1	1	2	1	1	6	2	4	2	9	5	27	3	2	4	7	2	1	59	3	1	2	1	1	2	2

Figure S31. Get High-res Image Gene #14: '7q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'7q gain' versus 'RADIATION_THERAPY'

P value = 0.00387 (Fisher's exact test), Q value = 0.07

Table S32. Gene #14: '7q gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	180	69
7Q GAIN MUTATED	39	28
7Q GAIN WILD-TYPE	141	41

Figure S32. Get High-res Image Gene #14: '7q gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

'7q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00059 (Fisher's exact test), Q value = 0.02

Table S33. 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	23	28	2	2	6	21
7Q GAIN MUTATED	11	0	0	19	2	11	14	0	0	0	11
7Q GAIN WILD-TYPE	48	2	1	84	7	12	14	2	2	6	10

Figure S33. Get High-res Image Gene #14: '7q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'8p gain' versus 'Time to Death'

P value = 0.00799 (logrank test), Q value = 0.1

Table S34. Gene #15: '8p gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	256	94	0.5 - 188.2 (26.4)
8P GAIN MUTATED	52	25	1.1 - 106.5 (19.2)
8P GAIN WILD-TYPE	204	69	0.5 - 188.2 (30.2)

Figure S34. Get High-res Image Gene #15: '8p gain' versus Clinical Feature #1: 'Time to Death'

'8p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0153 (Fisher's exact test), Q value = 0.13

Table S35. 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	23	28	2	2	6	21
8P GAIN MUTATED	4	0	0	22	1	9	8	0	0	0	8
8P GAIN WILD-TYPE	55	2	1	81	8	14	20	2	2	6	13

Figure S35. Get High-res Image Gene #15: '8p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'8p gain' versus 'RESIDUAL_TUMOR'

P value = 0.0388 (Fisher's exact test), Q value = 0.23

Table S36. Gene #15: '8p gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	152	68	9	26
8P GAIN MUTATED	26	20	3	2
8P GAIN WILD-TYPE	126	48	6	24

Figure S36. Get High-res Image Gene #15: '8p gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'8p gain' versus 'RACE'

P value = 0.0295 (Fisher's exact test), Q value = 0.2

Table S37. Gene #15: '8p gain' versus Clinical Feature #8: 'RACE'

nPatients	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	6	18	223
8P GAIN MUTATED	4	4	42
8P GAIN WILD-TYPE	2	14	181

Figure S37. Get High-res Image Gene #15: '8p gain' versus Clinical Feature #8: 'RACE'

'8q gain' versus 'Time to Death'

P value = 0.0132 (logrank test), Q value = 0.13

Table S38. Gene #16: '8q gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	256	94	0.5 - 188.2 (26.4)
8Q GAIN MUTATED	65	30	0.6 - 106.5 (22.6)
8Q GAIN WILD-TYPE	191	64	0.5 - 188.2 (29.9)

Figure S38. Get High-res Image Gene #16: '8q gain' versus Clinical Feature #1: 'Time to Death'

'9p gain' versus 'YEARS_TO_BIRTH'

P value = 0.00121 (Wilcoxon-test), Q value = 0.036

Table S39. Gene #17: '9p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
9P GAIN MUTATED	56	66.1 (14.5)
9P GAIN WILD-TYPE	199	59.5 (14.4)

Figure S39. Get High-res Image Gene #17: '9p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'9p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0122 (Fisher's exact test), Q value = 0.12

Table S40. 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	23	28	2	2	6	21
9P GAIN MUTATED	13	0	0	15	1	8	14	1	0	0	5
9P GAIN WILD-TYPE	46	2	1	88	8	15	14	1	2	6	16

Figure S40. Get High-res Image Gene #17: '9p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'9q gain' versus 'YEARS_TO_BIRTH'

P value = 7.38e-06 (Wilcoxon-test), Q value = 0.0011

Table S41. Gene #18: '9q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
9Q GAIN MUTATED	73	67.2 (14.0)
9Q GAIN WILD-TYPE	182	58.4 (14.2)

Figure S41. Get High-res Image Gene #18: '9q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'9q gain' versus 'TUMOR_TISSUE_SITE'

P value = 0.012 (Fisher's exact test), Q value = 0.12

Table S42. 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	43	4	2	5	8	2	1	73	3	2	5	4	1	7	5
9Q GAIN MUTATED	0	3	0	0	0	0	2	0	0	0	0	1	4	0	1	0	7	2	21	1	1	0	0	1	0	17	0	2	2	1	0	3	4
9Q GAIN WILD-TYPE	1	4	2	1	2	1	26	2	1	2	1	1	6	2	3	2	10	3	22	3	1	5	8	1	1	56	3	0	3	3	1	4	1

Figure S42. Get High-res Image Gene #18: '9q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'9q gain' versus 'HISTOLOGICAL_TYPE'

P value = 5e-05 (Fisher's exact test), Q value = 0.0034

Table S43. 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	23	28	2	2	6	21
9Q GAIN MUTATED	17	0	0	17	1	10	19	1	0	0	8
9Q GAIN WILD-TYPE	42	2	1	86	8	13	9	1	2	6	13

Figure S43. Get High-res Image Gene #18: '9q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'10p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0288 (Fisher's exact test), Q value = 0.2

Table S44. 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	23	28	2	2	6	21
10P GAIN MUTATED	2	0	0	6	0	5	6	1	0	0	3
10P GAIN WILD-TYPE	57	2	1	97	9	18	22	1	2	6	18

Figure S44. Get High-res Image Gene #19: '10p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'10q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0417 (Fisher's exact test), Q value = 0.24

Table S45. 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	23	28	2	2	6	21
10Q GAIN MUTATED	3	0	0	2	0	1	5	1	0	0	0
10Q GAIN WILD-TYPE	56	2	1	101	9	22	23	1	2	6	21

Figure S45. Get High-res Image Gene #20: '10q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'11p gain' versus 'Time to Death'

P value = 0.00534 (logrank test), Q value = 0.082

Table S46. Gene #21: '11p gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	256	94	0.5 - 188.2 (26.4)
11P GAIN MUTATED	23	14	1.1 - 123.8 (16.9)
11P GAIN WILD-TYPE	233	80	0.5 - 188.2 (28.2)

Figure S46. Get High-res Image Gene #21: '11p gain' versus Clinical Feature #1: 'Time to Death'

'11p gain' versus 'YEARS_TO_BIRTH'

P value = 4.57e-05 (Wilcoxon-test), Q value = 0.0034

Table S47. Gene #21: '11p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
11P GAIN MUTATED	23	72.0 (12.6)
11P GAIN WILD-TYPE	232	59.8 (14.4)

Figure S47. Get High-res Image Gene #21: '11p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'11p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0183 (Fisher's exact test), Q value = 0.15

Table S48. 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	23	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	17	21	2	2	6	20

Figure S48. Get High-res Image Gene #21: '11p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'11q gain' versus 'Time to Death'

P value = 0.00399 (logrank test), Q value = 0.07

Table S49. Gene #22: '11q gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	256	94	0.5 - 188.2 (26.4)
11Q GAIN MUTATED	22	14	1.1 - 123.8 (18.1)
11Q GAIN WILD-TYPE	234	80	0.5 - 188.2 (28.1)

Figure S49. Get High-res Image Gene #22: '11q gain' versus Clinical Feature #1: 'Time to Death'

'11q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0137 (Wilcoxon-test), Q value = 0.13

Table S50. Gene #22: '11q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
11Q GAIN MUTATED	22	67.6 (15.1)
11Q GAIN WILD-TYPE	233	60.3 (14.5)

Figure S50. Get High-res Image Gene #22: '11q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'12p gain' versus 'Time to Death'

P value = 0.00491 (logrank test), Q value = 0.077

Table S51. Gene #23: '12p gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	256	94	0.5 - 188.2 (26.4)
12P GAIN MUTATED	43	23	0.7 - 112.0 (17.5)
12P GAIN WILD-TYPE	213	71	0.5 - 188.2 (29.0)

Figure S51. Get High-res Image Gene #23: '12p gain' versus Clinical Feature #1: 'Time to Death'

'12p gain' versus 'YEARS_TO_BIRTH'

P value = 0.000179 (Wilcoxon-test), Q value = 0.0088

Table S52. Gene #23: '12p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
12P GAIN MUTATED	43	68.2 (13.0)
12P GAIN WILD-TYPE	212	59.5 (14.6)

Figure S52. Get High-res Image Gene #23: '12p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'12p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00037 (Fisher's exact test), Q value = 0.015

Table S53. 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	23	28	2	2	6	21
12P GAIN MUTATED	7	0	0	8	3	5	9	1	0	0	10
12P GAIN WILD-TYPE	52	2	1	95	6	18	19	1	2	6	11

Figure S53. Get High-res Image Gene #23: '12p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'12p gain' versus 'RACE'

P value = 0.0383 (Fisher's exact test), Q value = 0.23

Table S54. Gene #23: '12p gain' versus Clinical Feature #8: 'RACE'

nPatients	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	6	18	223
12P GAIN MUTATED	2	0	39
12P GAIN WILD-TYPE	4	18	184

Figure S54. Get High-res Image Gene #23: '12p gain' versus Clinical Feature #8: 'RACE'

'12q gain' versus 'RADIATION_THERAPY'

P value = 0.0373 (Fisher's exact test), Q value = 0.22

Table S55. Gene #24: '12q gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	180	69
12Q GAIN MUTATED	19	15
12Q GAIN WILD-TYPE	161	54

Figure S55. Get High-res Image Gene #24: '12q gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

'12q gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0011

Table S56. 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	23	28	2	2	6	21
12Q GAIN MUTATED	2	0	0	6	4	6	10	1	0	0	5
12Q GAIN WILD-TYPE	57	2	1	97	5	17	18	1	2	6	16

Figure S56. Get High-res Image Gene #24: '12q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'12q gain' versus 'RACE'

P value = 0.0121 (Fisher's exact test), Q value = 0.12

Table S57. Gene #24: '12q gain' versus Clinical Feature #8: 'RACE'

nPatients	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	6	18	223
12Q GAIN MUTATED	3	0	29
12Q GAIN WILD-TYPE	3	18	194

Figure S57. Get High-res Image Gene #24: '12q gain' versus Clinical Feature #8: 'RACE'

'13q gain' versus 'RACE'

P value = 0.023 (Fisher's exact test), Q value = 0.17

Table S58. Gene #25: '13q gain' versus Clinical Feature #8: 'RACE'

nPatients	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	6	18	223
13Q GAIN MUTATED	0	4	10
13Q GAIN WILD-TYPE	6	14	213

Figure S58. Get High-res Image Gene #25: '13q gain' versus Clinical Feature #8: 'RACE'

'14q gain' versus 'Time to Death'

P value = 0.0233 (logrank test), Q value = 0.17

Table S59. Gene #26: '14q gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	256	94	0.5 - 188.2 (26.4)
14Q GAIN MUTATED	57	29	0.6 - 124.7 (21.3)
14Q GAIN WILD-TYPE	199	65	0.5 - 188.2 (29.0)

Figure S59. Get High-res Image Gene #26: '14q gain' versus Clinical Feature #1: 'Time to Death'

'14q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0063 (Wilcoxon-test), Q value = 0.089

Table S60. Gene #26: '14q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
14Q GAIN MUTATED	57	65.6 (15.2)
14Q GAIN WILD-TYPE	198	59.6 (14.3)

Figure S60. Get High-res Image Gene #26: '14q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'14q gain' versus 'TUMOR_TISSUE_SITE'

P value = 0.0088 (Fisher's exact test), Q value = 0.1

Table S61. 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	43	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	6	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	11	2	30	4	1	5	5	1	1	64	3	0	3	4	1	5	3

Figure S61. Get High-res Image Gene #26: '14q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'15q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0349 (Wilcoxon-test), Q value = 0.22

Table S62. Gene #27: '15q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
15Q GAIN MUTATED	63	64.3 (13.6)
15Q GAIN WILD-TYPE	192	59.8 (14.9)

Figure S62. Get High-res Image Gene #27: '15q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'16p gain' versus 'Time to Death'

P value = 0.0155 (logrank test), Q value = 0.13

Table S63. Gene #28: '16p gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	256	94	0.5 - 188.2 (26.4)
16P GAIN MUTATED	40	22	3.9 - 86.1 (26.7)
16P GAIN WILD-TYPE	216	72	0.5 - 188.2 (26.3)

Figure S63. Get High-res Image Gene #28: '16p gain' versus Clinical Feature #1: 'Time to Death'

'16p gain' versus 'YEARS_TO_BIRTH'

P value = 0.0142 (Wilcoxon-test), Q value = 0.13

Table S64. Gene #28: '16p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
16P GAIN MUTATED	40	66.2 (13.6)
16P GAIN WILD-TYPE	215	59.9 (14.7)

Figure S64. Get High-res Image Gene #28: '16p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'16p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.025 (Fisher's exact test), Q value = 0.18

Table S65. 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	23	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	16	18	2	2	6	21

Figure S65. Get High-res Image Gene #28: '16p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'17p gain' versus 'YEARS_TO_BIRTH'

P value = 0.0351 (Wilcoxon-test), Q value = 0.22

Table S66. Gene #30: '17p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
17P GAIN MUTATED	60	64.7 (13.0)
17P GAIN WILD-TYPE	195	59.8 (15.0)

Figure S66. Get High-res Image Gene #30: '17p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'17q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00288 (Fisher's exact test), Q value = 0.059

Table S67. 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	23	28	2	2	6	21
17Q GAIN MUTATED	6	0	0	19	2	11	10	0	0	0	9
17Q GAIN WILD-TYPE	53	2	1	84	7	12	18	2	2	6	12

Figure S67. Get High-res Image Gene #31: '17q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'18p gain' versus 'YEARS_TO_BIRTH'

P value = 0.0127 (Wilcoxon-test), Q value = 0.13

Table S68. Gene #32: '18p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
18P GAIN MUTATED	53	65.4 (12.4)
18P GAIN WILD-TYPE	202	59.8 (15.0)

Figure S68. Get High-res Image Gene #32: '18p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'18p gain' versus 'RADIATION_THERAPY'

P value = 0.00152 (Fisher's exact test), Q value = 0.043

Table S69. Gene #32: '18p gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	180	69
18P GAIN MUTATED	28	24
18P GAIN WILD-TYPE	152	45

Figure S69. Get High-res Image Gene #32: '18p gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

'18p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.023 (Fisher's exact test), Q value = 0.17

Table S70. Gene #32: '18p 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	23	28	2	2	6	21
18P GAIN MUTATED	5	0	0	20	2	7	11	0	0	0	8
18P GAIN WILD-TYPE	54	2	1	83	7	16	17	2	2	6	13

Figure S70. Get High-res Image Gene #32: '18p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'18q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0262 (Wilcoxon-test), Q value = 0.19

Table S71. Gene #33: '18q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
18Q GAIN MUTATED	35	65.7 (14.5)
18Q GAIN WILD-TYPE	220	60.2 (14.6)

Figure S71. Get High-res Image Gene #33: '18q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'19p gain' versus 'YEARS_TO_BIRTH'

P value = 0.000107 (Wilcoxon-test), Q value = 0.0061

Table S72. Gene #34: '19p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
19P GAIN MUTATED	86	65.7 (12.8)
19P GAIN WILD-TYPE	169	58.5 (15.0)

Figure S72. Get High-res Image Gene #34: '19p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'19p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00453 (Fisher's exact test), Q value = 0.073

Table S73. 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	23	28	2	2	6	21
19P GAIN MUTATED	19	0	0	27	3	9	18	0	0	0	11
19P GAIN WILD-TYPE	40	2	1	76	6	14	10	2	2	6	10

Figure S73. Get High-res Image Gene #34: '19p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'19q gain' versus 'YEARS_TO_BIRTH'

P value = 0.00428 (Wilcoxon-test), Q value = 0.072

Table S74. Gene #35: '19q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
19Q GAIN MUTATED	64	65.5 (12.6)
19Q GAIN WILD-TYPE	191	59.4 (15.0)

Figure S74. Get High-res Image Gene #35: '19q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'19q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00679 (Fisher's exact test), Q value = 0.093

Table S75. 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	23	28	2	2	6	21
19Q GAIN MUTATED	14	0	0	19	0	11	12	0	0	0	9
19Q GAIN WILD-TYPE	45	2	1	84	9	12	16	2	2	6	12

Figure S75. Get High-res Image Gene #35: '19q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'20p gain' versus 'Time to Death'

P value = 0.000481 (logrank test), Q value = 0.018

Table S76. Gene #36: '20p gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	256	94	0.5 - 188.2 (26.4)
20P GAIN MUTATED	62	32	0.6 - 106.5 (23.5)
20P GAIN WILD-TYPE	194	62	0.5 - 188.2 (29.2)

Figure S76. Get High-res Image Gene #36: '20p gain' versus Clinical Feature #1: 'Time to Death'

'20p gain' versus 'YEARS_TO_BIRTH'

P value = 0.0111 (Wilcoxon-test), Q value = 0.12

Table S77. Gene #36: '20p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
20P GAIN MUTATED	62	65.4 (13.8)
20P GAIN WILD-TYPE	193	59.5 (14.7)

Figure S77. Get High-res Image Gene #36: '20p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'20q gain' versus 'Time to Death'

P value = 0.00452 (logrank test), Q value = 0.073

Table S78. Gene #37: '20q gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	256	94	0.5 - 188.2 (26.4)
20Q GAIN MUTATED	83	40	0.6 - 143.4 (22.9)
20Q GAIN WILD-TYPE	173	54	0.5 - 188.2 (29.5)

Figure S78. Get High-res Image Gene #37: '20q gain' versus Clinical Feature #1: 'Time to Death'

'20q gain' versus 'YEARS_TO_BIRTH'

P value = 0.000237 (Wilcoxon-test), Q value = 0.011

Table S79. Gene #37: '20q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
20Q GAIN MUTATED	83	65.9 (13.1)
20Q GAIN WILD-TYPE	172	58.5 (14.8)

Figure S79. Get High-res Image Gene #37: '20q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'20q gain' versus 'GENDER'

P value = 0.0076 (Fisher's exact test), Q value = 0.1

Table S80. Gene #37: '20q gain' versus Clinical Feature #4: 'GENDER'

nPatients	FEMALE	MALE
ALL	139	117
20Q GAIN MUTATED	35	48
20Q GAIN WILD-TYPE	104	69

Figure S80. Get High-res Image Gene #37: '20q gain' versus Clinical Feature #4: 'GENDER'

'20q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00695 (Fisher's exact test), Q value = 0.093

Table S81. 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	23	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	11	12	2	2	6	11

Figure S81. Get High-res Image Gene #37: '20q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'21q gain' versus 'Time to Death'

P value = 0.0181 (logrank test), Q value = 0.15

Table S82. Gene #38: '21q gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	256	94	0.5 - 188.2 (26.4)
21Q GAIN MUTATED	58	28	0.7 - 124.7 (24.4)
21Q GAIN WILD-TYPE	198	66	0.5 - 188.2 (27.4)

Figure S82. Get High-res Image Gene #38: '21q gain' versus Clinical Feature #1: 'Time to Death'

'21q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0198 (Wilcoxon-test), Q value = 0.16

Table S83. Gene #38: '21q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
21Q GAIN MUTATED	57	65.0 (12.1)
21Q GAIN WILD-TYPE	198	59.8 (15.2)

Figure S83. Get High-res Image Gene #38: '21q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'22q gain' versus 'YEARS_TO_BIRTH'

P value = 0.00163 (Wilcoxon-test), Q value = 0.043

Table S84. Gene #39: '22q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
22Q GAIN MUTATED	60	66.0 (12.9)
22Q GAIN WILD-TYPE	195	59.4 (14.9)

Figure S84. Get High-res Image Gene #39: '22q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'22q gain' versus 'RADIATION_THERAPY'

P value = 0.0311 (Fisher's exact test), Q value = 0.2

Table S85. Gene #39: '22q gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	180	69
22Q GAIN MUTATED	36	23
22Q GAIN WILD-TYPE	144	46

Figure S85. Get High-res Image Gene #39: '22q gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

'xp gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0428 (Fisher's exact test), Q value = 0.25

Table S86. 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	23	28	2	2	6	21
XP GAIN MUTATED	11	0	0	29	1	11	12	1	0	0	9
XP GAIN WILD-TYPE	48	2	1	74	8	12	16	1	2	6	12

Figure S86. Get High-res Image Gene #40: 'xp gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'xq gain' versus 'ETHNICITY'

P value = 0.0162 (Fisher's exact test), Q value = 0.14

Table S87. Gene #41: 'xq gain' versus Clinical Feature #9: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	5	220
XQ GAIN MUTATED	3	26
XQ GAIN WILD-TYPE	2	194

Figure S87. Get High-res Image Gene #41: 'xq gain' versus Clinical Feature #9: 'ETHNICITY'

'1p loss' versus 'GENDER'

P value = 0.0135 (Fisher's exact test), Q value = 0.13

Table S88. Gene #42: '1p loss' versus Clinical Feature #4: 'GENDER'

nPatients	FEMALE	MALE
ALL	139	117
1P LOSS MUTATED	24	8
1P LOSS WILD-TYPE	115	109

Figure S88. Get High-res Image Gene #42: '1p loss' versus Clinical Feature #4: 'GENDER'

'1q loss' versus 'RADIATION_THERAPY'

P value = 0.0328 (Fisher's exact test), Q value = 0.21

Table S89. Gene #43: '1q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	180	69
1Q LOSS MUTATED	23	17
1Q LOSS WILD-TYPE	157	52

Figure S89. Get High-res Image Gene #43: '1q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'2p loss' versus 'YEARS_TO_BIRTH'

P value = 0.00571 (Wilcoxon-test), Q value = 0.084

Table S90. Gene #44: '2p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
2P LOSS MUTATED	87	64.6 (13.6)
2P LOSS WILD-TYPE	168	59.0 (14.9)

Figure S90. Get High-res Image Gene #44: '2p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'2p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0058 (Fisher's exact test), Q value = 0.084

Table S91. 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	23	28	2	2	6	21
2P LOSS MUTATED	11	0	0	42	1	10	13	0	0	0	11
2P LOSS WILD-TYPE	48	2	1	61	8	13	15	2	2	6	10

Figure S91. Get High-res Image Gene #44: '2p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'2p loss' versus 'RACE'

P value = 0.0322 (Fisher's exact test), Q value = 0.21

Table S92. Gene #44: '2p loss' versus Clinical Feature #8: 'RACE'

nPatients	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	6	18	223
2P LOSS MUTATED	0	10	72
2P LOSS WILD-TYPE	6	8	151

Figure S92. Get High-res Image Gene #44: '2p loss' versus Clinical Feature #8: 'RACE'

'2q loss' versus 'Time to Death'

P value = 0.000721 (logrank test), Q value = 0.022

Table S93. Gene #45: '2q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	256	94	0.5 - 188.2 (26.4)
2Q LOSS MUTATED	71	33	0.7 - 106.5 (18.9)
2Q LOSS WILD-TYPE	185	61	0.5 - 188.2 (31.3)

Figure S93. Get High-res Image Gene #45: '2q loss' versus Clinical Feature #1: 'Time to Death'

'2q loss' versus 'YEARS_TO_BIRTH'

P value = 0.000297 (Wilcoxon-test), Q value = 0.013

Table S94. Gene #45: '2q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
2Q LOSS MUTATED	70	66.2 (13.4)
2Q LOSS WILD-TYPE	185	58.9 (14.7)

Figure S94. Get High-res Image Gene #45: '2q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'3p loss' versus 'YEARS_TO_BIRTH'

P value = 0.013 (Wilcoxon-test), Q value = 0.13

Table S95. Gene #46: '3p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
3P LOSS MUTATED	56	64.7 (15.7)
3P LOSS WILD-TYPE	199	59.9 (14.3)

Figure S95. Get High-res Image Gene #46: '3p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'3p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00567 (Fisher's exact test), Q value = 0.084

Table S96. 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	23	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	15	18	2	0	4	16

Figure S96. Get High-res Image Gene #46: '3p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'3q loss' versus 'Time to Death'

P value = 0.0361 (logrank test), Q value = 0.22

Table S97. Gene #47: '3q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	256	94	0.5 - 188.2 (26.4)
3Q LOSS MUTATED	49	23	1.1 - 188.2 (21.7)
3Q LOSS WILD-TYPE	207	71	0.5 - 143.4 (28.2)

Figure S97. Get High-res Image Gene #47: '3q loss' versus Clinical Feature #1: 'Time to Death'

'3q loss' versus 'YEARS_TO_BIRTH'

P value = 0.00939 (Wilcoxon-test), Q value = 0.11

Table S98. Gene #47: '3q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
3Q LOSS MUTATED	49	65.3 (14.7)
3Q LOSS WILD-TYPE	206	59.9 (14.5)

Figure S98. Get High-res Image Gene #47: '3q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'4p loss' versus 'RADIATION_THERAPY'

P value = 0.0207 (Fisher's exact test), Q value = 0.16

Table S99. Gene #48: '4p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	180	69
4P LOSS MUTATED	23	18
4P LOSS WILD-TYPE	157	51

Figure S99. Get High-res Image Gene #48: '4p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'4q loss' versus 'RADIATION_THERAPY'

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

Table S100. Gene #49: '4q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	180	69
4Q LOSS MUTATED	30	20
4Q LOSS WILD-TYPE	150	49

Figure S100. Get High-res Image Gene #49: '4q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'6p loss' versus 'Time to Death'

P value = 0.00159 (logrank test), Q value = 0.043

Table S101. Gene #52: '6p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	256	94	0.5 - 188.2 (26.4)
6P LOSS MUTATED	60	12	4.4 - 188.2 (34.0)
6P LOSS WILD-TYPE	196	82	0.5 - 143.4 (25.2)

Figure S101. Get High-res Image Gene #52: '6p loss' versus Clinical Feature #1: 'Time to Death'

'8q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0367 (Wilcoxon-test), Q value = 0.22

Table S102. Gene #57: '8q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
8Q LOSS MUTATED	46	65.1 (12.9)
8Q LOSS WILD-TYPE	209	60.0 (14.9)

Figure S102. Get High-res Image Gene #57: '8q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'9p loss' versus 'YEARS_TO_BIRTH'

P value = 0.00249 (Wilcoxon-test), Q value = 0.056

Table S103. Gene #58: '9p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
9P LOSS MUTATED	83	64.9 (13.4)
9P LOSS WILD-TYPE	172	59.0 (14.9)

Figure S103. Get High-res Image Gene #58: '9p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'10p loss' versus 'YEARS_TO_BIRTH'

P value = 0.0184 (Wilcoxon-test), Q value = 0.15

Table S104. Gene #60: '10p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
10P LOSS MUTATED	120	63.2 (14.5)
10P LOSS WILD-TYPE	135	58.9 (14.6)

Figure S104. Get High-res Image Gene #60: '10p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'10p loss' versus 'GENDER'

P value = 0.00821 (Fisher's exact test), Q value = 0.1

Table S105. Gene #60: '10p loss' versus Clinical Feature #4: 'GENDER'

nPatients	FEMALE	MALE
ALL	139	117
10P LOSS MUTATED	76	44
10P LOSS WILD-TYPE	63	73

Figure S105. Get High-res Image Gene #60: '10p loss' versus Clinical Feature #4: 'GENDER'

'10p loss' versus 'HISTOLOGICAL_TYPE'

P value = 2e-05 (Fisher's exact test), Q value = 0.0016

Table S106. 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	23	28	2	2	6	21
10P LOSS MUTATED	12	0	0	60	7	13	14	0	0	1	13
10P LOSS WILD-TYPE	47	2	1	43	2	10	14	2	2	5	8

Figure S106. Get High-res Image Gene #60: '10p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'10q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0101 (Wilcoxon-test), Q value = 0.12

Table S107. Gene #61: '10q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
10Q LOSS MUTATED	131	63.5 (13.3)
10Q LOSS WILD-TYPE	124	58.3 (15.6)

Figure S107. Get High-res Image Gene #61: '10q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'10q loss' versus 'GENDER'

P value = 0.00831 (Fisher's exact test), Q value = 0.1

Table S108. Gene #61: '10q loss' versus Clinical Feature #4: 'GENDER'

nPatients	FEMALE	MALE
ALL	139	117
10Q LOSS MUTATED	82	49
10Q LOSS WILD-TYPE	57	68

Figure S108. 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 = 0.0011

Table S109. 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	23	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	9	13	2	2	6	6

Figure S109. Get High-res Image Gene #61: '10q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'11q loss' versus 'RADIATION_THERAPY'

P value = 0.0192 (Fisher's exact test), Q value = 0.16

Table S110. Gene #63: '11q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	180	69
11Q LOSS MUTATED	57	33
11Q LOSS WILD-TYPE	123	36

Figure S110. Get High-res Image Gene #63: '11q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'13q loss' versus 'YEARS_TO_BIRTH'

P value = 0.00174 (Wilcoxon-test), Q value = 0.044

Table S111. Gene #66: '13q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
13Q LOSS MUTATED	132	63.7 (14.0)
13Q LOSS WILD-TYPE	123	57.9 (14.8)

Figure S111. Get High-res Image Gene #66: '13q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'13q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0149 (Fisher's exact test), Q value = 0.13

Table S112. 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	23	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	10	10	2	2	5	7

Figure S112. Get High-res Image Gene #66: '13q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'15q loss' versus 'Time to Death'

P value = 0.000172 (logrank test), Q value = 0.0088

Table S113. Gene #68: '15q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	256	94	0.5 - 188.2 (26.4)
15Q LOSS MUTATED	45	26	3.1 - 143.4 (19.9)
15Q LOSS WILD-TYPE	211	68	0.5 - 188.2 (28.2)

Figure S113. Get High-res Image Gene #68: '15q loss' versus Clinical Feature #1: 'Time to Death'

'15q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0194 (Wilcoxon-test), Q value = 0.16

Table S114. Gene #68: '15q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
15Q LOSS MUTATED	45	65.6 (13.4)
15Q LOSS WILD-TYPE	210	59.9 (14.8)

Figure S114. Get High-res Image Gene #68: '15q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'16p loss' versus 'HISTOLOGICAL_TYPE'

P value = 2e-05 (Fisher's exact test), Q value = 0.0016

Table S115. 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	23	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	18	17	2	2	6	4

Figure S115. Get High-res Image Gene #69: '16p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'16q loss' versus 'YEARS_TO_BIRTH'

P value = 0.00278 (Wilcoxon-test), Q value = 0.059

Table S116. Gene #70: '16q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
16Q LOSS MUTATED	123	63.6 (13.7)
16Q LOSS WILD-TYPE	132	58.5 (15.2)

Figure S116. 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 = 0.0011

Table S117. 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	23	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	14	12	2	1	6	4

Figure S117. Get High-res Image Gene #70: '16q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'17q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0268 (Wilcoxon-test), Q value = 0.19

Table S118. Gene #72: '17q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
17Q LOSS MUTATED	48	64.2 (16.2)
17Q LOSS WILD-TYPE	207	60.2 (14.2)

Figure S118. Get High-res Image Gene #72: '17q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'17q loss' versus 'RADIATION_THERAPY'

P value = 0.0107 (Fisher's exact test), Q value = 0.12

Table S119. Gene #72: '17q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	180	69
17Q LOSS MUTATED	26	20
17Q LOSS WILD-TYPE	154	49

Figure S119. Get High-res Image Gene #72: '17q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'18q loss' versus 'Time to Death'

P value = 0.0297 (logrank test), Q value = 0.2

Table S120. Gene #74: '18q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	256	94	0.5 - 188.2 (26.4)
18Q LOSS MUTATED	72	33	0.6 - 188.2 (22.6)
18Q LOSS WILD-TYPE	184	61	0.5 - 135.5 (28.6)

Figure S120. Get High-res Image Gene #74: '18q loss' versus Clinical Feature #1: 'Time to Death'

'18q loss' versus 'RADIATION_THERAPY'

P value = 0.0279 (Fisher's exact test), Q value = 0.19

Table S121. Gene #74: '18q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	180	69
18Q LOSS MUTATED	44	27
18Q LOSS WILD-TYPE	136	42

Figure S121. Get High-res Image Gene #74: '18q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'18q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0193 (Fisher's exact test), Q value = 0.16

Table S122. Gene #74: '18q 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	23	28	2	2	6	21
18Q LOSS MUTATED	13	0	0	23	6	10	12	0	0	0	8
18Q LOSS WILD-TYPE	46	2	1	80	3	13	16	2	2	6	13

Figure S122. Get High-res Image Gene #74: '18q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'19p loss' versus 'RADIATION_THERAPY'

P value = 0.0037 (Fisher's exact test), Q value = 0.07

Table S123. Gene #75: '19p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	180	69
19P LOSS MUTATED	9	12
19P LOSS WILD-TYPE	171	57

Figure S123. Get High-res Image Gene #75: '19p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'20p loss' versus 'YEARS_TO_BIRTH'

P value = 0.00363 (Wilcoxon-test), Q value = 0.07

Table S124. Gene #77: '20p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
20P LOSS MUTATED	55	65.7 (11.6)
20P LOSS WILD-TYPE	200	59.6 (15.2)

Figure S124. Get High-res Image Gene #77: '20p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'20p loss' versus 'RADIATION_THERAPY'

P value = 0.0105 (Fisher's exact test), Q value = 0.12

Table S125. Gene #77: '20p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	180	69
20P LOSS MUTATED	32	23
20P LOSS WILD-TYPE	148	46

Figure S125. Get High-res Image Gene #77: '20p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'20q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0224 (Wilcoxon-test), Q value = 0.17

Table S126. Gene #78: '20q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
20Q LOSS MUTATED	25	67.4 (10.6)
20Q LOSS WILD-TYPE	230	60.2 (14.9)

Figure S126. Get High-res Image Gene #78: '20q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'21q loss' versus 'YEARS_TO_BIRTH'

P value = 0.031 (Wilcoxon-test), Q value = 0.2

Table S127. Gene #79: '21q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	255	60.9 (14.7)
21Q LOSS MUTATED	50	65.1 (11.9)
21Q LOSS WILD-TYPE	205	59.9 (15.1)

Figure S127. Get High-res Image Gene #79: '21q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'xq loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00038 (Fisher's exact test), Q value = 0.015

Table S128. 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	23	28	2	2	6	21
XQ LOSS MUTATED	14	0	0	57	5	4	10	0	0	1	10
XQ LOSS WILD-TYPE	45	2	1	46	4	19	18	2	2	5	11

Figure S128. 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/19782152/transformed.cor.cli.txt
Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/SARC-TP/19775498/SARC-TP.merged_data.txt
Number of patients = 256
Number of significantly 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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