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

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 81 arm-level events and 8 clinical features across 512 patients, 157 significant findings detected with Q value < 0.25.

1p gain cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.
1q gain cnv correlated to 'YEARS_TO_BIRTH'.
3p gain cnv correlated to 'Time to Death' and 'HISTOLOGICAL_TYPE'.
3q gain cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.
4q gain cnv correlated to 'YEARS_TO_BIRTH'.
5p gain cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.
5q gain cnv correlated to 'Time to Death' and 'RACE'.
7p gain cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'RADIATION_THERAPY', 'KARNOFSKY_PERFORMANCE_SCORE', and 'RACE'.
7q gain cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'RADIATION_THERAPY', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', and 'RACE'.
8q gain cnv correlated to 'RADIATION_THERAPY'.
9p gain cnv correlated to 'GENDER' and 'RADIATION_THERAPY'.
9q gain cnv correlated to 'GENDER', 'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.
10p gain cnv correlated to 'YEARS_TO_BIRTH', 'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.
10q gain cnv correlated to 'HISTOLOGICAL_TYPE'.
11p gain cnv correlated to 'YEARS_TO_BIRTH' and 'HISTOLOGICAL_TYPE'.
12p gain cnv correlated to 'RADIATION_THERAPY'.
12q gain cnv correlated to 'Time to Death'.
13q gain cnv correlated to 'RADIATION_THERAPY'.
15q gain cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', and 'KARNOFSKY_PERFORMANCE_SCORE'.
16p gain cnv correlated to 'YEARS_TO_BIRTH'.
16q gain cnv correlated to 'HISTOLOGICAL_TYPE'.
17p gain cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', and 'HISTOLOGICAL_TYPE'.
17q gain cnv correlated to 'Time to Death'.
18p gain cnv correlated to 'Time to Death'.
18q gain cnv correlated to 'Time to Death'.
19p gain cnv correlated to 'YEARS_TO_BIRTH', 'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.
19q gain cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.
20p gain cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'RADIATION_THERAPY', and 'KARNOFSKY_PERFORMANCE_SCORE'.
20q gain cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'RADIATION_THERAPY', and 'KARNOFSKY_PERFORMANCE_SCORE'.
21q gain cnv correlated to 'YEARS_TO_BIRTH'.
22q gain cnv correlated to 'YEARS_TO_BIRTH' and 'HISTOLOGICAL_TYPE'.
xp gain cnv correlated to 'HISTOLOGICAL_TYPE'.
xq gain cnv correlated to 'YEARS_TO_BIRTH', 'GENDER', 'HISTOLOGICAL_TYPE', and 'ETHNICITY'.
1p loss cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.
1q loss cnv correlated to 'HISTOLOGICAL_TYPE'.
2p loss cnv correlated to 'RADIATION_THERAPY'.
2q loss cnv correlated to 'HISTOLOGICAL_TYPE'.
3p loss cnv correlated to 'Time to Death' and 'KARNOFSKY_PERFORMANCE_SCORE'.
3q loss cnv correlated to 'Time to Death'.
4p loss cnv correlated to 'YEARS_TO_BIRTH', 'GENDER', and 'HISTOLOGICAL_TYPE'.
4q loss cnv correlated to 'HISTOLOGICAL_TYPE'.
5p loss cnv correlated to 'RADIATION_THERAPY' and 'HISTOLOGICAL_TYPE'.
5q loss cnv correlated to 'RADIATION_THERAPY' and 'HISTOLOGICAL_TYPE'.
6p loss cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', and 'RADIATION_THERAPY'.
6q loss cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'RADIATION_THERAPY', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', and 'RACE'.
8p loss cnv correlated to 'Time to Death'.
8q loss cnv correlated to 'Time to Death'.
9p loss cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'RADIATION_THERAPY', 'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.
9q loss cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'RADIATION_THERAPY', and 'KARNOFSKY_PERFORMANCE_SCORE'.
10p loss cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'RADIATION_THERAPY', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', and 'RACE'.
10q loss cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'RADIATION_THERAPY', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', and 'RACE'.
11p loss cnv correlated to 'Time to Death', 'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.
11q loss cnv correlated to 'Time to Death' and 'HISTOLOGICAL_TYPE'.
12q loss cnv correlated to 'HISTOLOGICAL_TYPE'.
13q loss cnv correlated to 'RADIATION_THERAPY'.
14q loss cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', and 'KARNOFSKY_PERFORMANCE_SCORE'.
16p loss cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.
16q loss cnv correlated to 'YEARS_TO_BIRTH' and 'RADIATION_THERAPY'.
17p loss cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'KARNOFSKY_PERFORMANCE_SCORE', and 'ETHNICITY'.
18p loss cnv correlated to 'YEARS_TO_BIRTH'.
18q loss cnv correlated to 'YEARS_TO_BIRTH' and 'HISTOLOGICAL_TYPE'.
19p loss cnv correlated to 'RACE' and 'ETHNICITY'.
19q loss cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.
20p loss cnv correlated to 'RADIATION_THERAPY'.
21q loss cnv correlated to 'KARNOFSKY_PERFORMANCE_SCORE' and 'HISTOLOGICAL_TYPE'.
22q loss cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'RADIATION_THERAPY', and 'KARNOFSKY_PERFORMANCE_SCORE'.
xq loss cnv correlated to 'Time to Death'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 81 arm-level events and 8 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 157 significant findings detected.


		Clinical Features	Time to Death	YEARS TO BIRTH	GENDER	RADIATION THERAPY	KARNOFSKY PERFORMANCE SCORE	HISTOLOGICAL TYPE	RACE	ETHNICITY
	nCNV (%)	nWild-Type	logrank test	Wilcoxon-test	Fisher's exact test	Fisher's exact test	Wilcoxon-test	Fisher's exact test	Fisher's exact test	Fisher's exact test
7q gain	150 (29%)	362	2.81e-07 (1.21e-05)	1.96e-10 (1.82e-08)	0.435 (0.775)	0.00116 (0.0153)	0.00576 (0.0541)	0.0514 (0.228)	0.00939 (0.0761)	0.557 (0.849)
6q loss	62 (12%)	450	7.35e-05 (0.0017)	0.0291 (0.161)	0.414 (0.755)	0.0253 (0.15)	0.00121 (0.0157)	0.00115 (0.0153)	0.0504 (0.225)	0.563 (0.849)
10p loss	83 (16%)	429	0 (0)	5.96e-20 (1.29e-17)	0.81 (0.973)	9.18e-05 (0.00205)	0.000203 (0.00387)	0.00011 (0.0022)	0.00867 (0.0723)	0.804 (0.973)
10q loss	97 (19%)	415	0 (0)	2.9e-17 (4.69e-15)	0.734 (0.942)	2.96e-06 (0.000107)	0.000212 (0.0039)	3e-05 (0.000778)	0.0278 (0.159)	0.485 (0.813)
7p gain	120 (23%)	392	9.05e-08 (4.89e-06)	1.63e-10 (1.76e-08)	0.174 (0.457)	0.000773 (0.0111)	0.000962 (0.0133)	0.239 (0.553)	0.0159 (0.106)	0.834 (0.986)
9p loss	117 (23%)	395	1.11e-06 (4.48e-05)	0.00204 (0.0245)	1 (1.00)	0.000609 (0.00918)	0.00199 (0.0243)	0.0589 (0.247)	0.605 (0.875)	0.669 (0.896)
1p gain	13 (3%)	499	0.016 (0.106)	0.0126 (0.0946)	0.263 (0.578)	0.0344 (0.175)	0.799 (0.973)	0.00907 (0.0744)	0.556 (0.849)	1 (1.00)
20p gain	45 (9%)	467	2.94e-12 (3.8e-10)	7.25e-09 (5.22e-07)	0.757 (0.957)	0.0282 (0.159)	0.00967 (0.0764)	0.186 (0.473)	0.47 (0.804)	0.343 (0.668)
20q gain	44 (9%)	468	2.04e-09 (1.65e-07)	2.04e-08 (1.2e-06)	0.341 (0.668)	0.0282 (0.159)	0.0145 (0.102)	0.234 (0.549)	0.64 (0.885)	0.507 (0.819)
xq gain	41 (8%)	471	0.159 (0.433)	0.0539 (0.236)	0.0136 (0.1)	0.229 (0.549)	0.519 (0.831)	0.00437 (0.0442)	0.611 (0.875)	0.0254 (0.15)
1p loss	184 (36%)	328	0.000112 (0.0022)	0.000914 (0.0129)	0.853 (1.00)	1.83e-07 (8.9e-06)	0.293 (0.615)	1e-05 (0.000282)	0.315 (0.636)	0.704 (0.924)
9q loss	50 (10%)	462	0.0035 (0.0372)	0.00595 (0.0551)	1 (1.00)	0.011 (0.084)	0.000364 (0.0059)	0.877 (1.00)	0.136 (0.403)	1 (1.00)
17p loss	14 (3%)	498	0.0587 (0.247)	0.0397 (0.196)	0.174 (0.457)	1 (1.00)	0.0168 (0.109)	0.551 (0.849)	1 (1.00)	0.0599 (0.247)
19q loss	209 (41%)	303	0.0024 (0.0273)	0.0437 (0.207)	0.928 (1.00)	4.3e-06 (0.000147)	0.353 (0.681)	1e-05 (0.000282)	0.918 (1.00)	0.0929 (0.328)
22q loss	57 (11%)	455	1.94e-08 (1.2e-06)	2.06e-06 (7.84e-05)	0.482 (0.813)	0.0483 (0.22)	0.00505 (0.0496)	0.121 (0.375)	0.173 (0.457)	0.56 (0.849)
9q gain	24 (5%)	488	0.373 (0.713)	0.0775 (0.299)	0.00268 (0.03)	0.00177 (0.0225)	0.557 (0.849)	0.0586 (0.247)	0.212 (0.521)	0.661 (0.892)
10p gain	57 (11%)	455	0.536 (0.848)	0.0215 (0.131)	0.258 (0.576)	0.0159 (0.106)	0.217 (0.53)	0.00026 (0.00443)	1 (1.00)	0.136 (0.403)
15q gain	11 (2%)	501	0.0166 (0.109)	0.0259 (0.15)	1 (1.00)	0.543 (0.848)	0.0135 (0.1)	0.406 (0.748)	0.496 (0.815)	1 (1.00)
17p gain	20 (4%)	492	0.0143 (0.102)	0.0176 (0.112)	0.106 (0.355)	0.49 (0.813)	0.678 (0.901)	0.059 (0.247)	0.223 (0.54)	1 (1.00)
19p gain	99 (19%)	413	0.629 (0.885)	0.00964 (0.0764)	0.262 (0.578)	0.043 (0.206)	0.464 (0.802)	1e-05 (0.000282)	0.5 (0.816)	0.108 (0.36)
4p loss	72 (14%)	440	0.74 (0.945)	0.0188 (0.118)	0.0413 (0.201)	1 (1.00)	0.956 (1.00)	0.00049 (0.00774)	0.562 (0.849)	0.798 (0.973)
6p loss	30 (6%)	482	0.000108 (0.0022)	0.0548 (0.237)	0.573 (0.853)	0.0583 (0.247)	0.0745 (0.289)	0.233 (0.549)	0.0616 (0.252)	1 (1.00)
11p loss	63 (12%)	449	0.0307 (0.166)	0.265 (0.58)	0.343 (0.668)	0.00629 (0.0574)	0.168 (0.45)	0.00063 (0.00928)	0.562 (0.849)	0.784 (0.972)
14q loss	81 (16%)	431	2.47e-05 (0.000666)	3.84e-05 (0.000958)	1 (1.00)	0.194 (0.481)	0.035 (0.177)	0.2 (0.495)	0.218 (0.53)	0.452 (0.795)
3p gain	11 (2%)	501	0.039 (0.194)	0.0849 (0.311)	0.551 (0.849)	1 (1.00)	0.805 (0.973)	0.0288 (0.161)	1 (1.00)	1 (1.00)
3q gain	8 (2%)	504	0.0022 (0.0259)	0.0332 (0.172)	0.476 (0.81)	0.414 (0.755)	0.302 (0.621)	0.0914 (0.325)	1 (1.00)	1 (1.00)
5p gain	11 (2%)	501	0.0305 (0.166)	0.0321 (0.17)	1 (1.00)	0.543 (0.848)	0.791 (0.973)	0.243 (0.555)	0.079 (0.301)	1 (1.00)
5q gain	9 (2%)	503	0.042 (0.203)	0.0627 (0.256)	0.521 (0.831)	1 (1.00)	0.97 (1.00)	0.584 (0.857)	0.0548 (0.237)	1 (1.00)
9p gain	17 (3%)	495	0.58 (0.857)	0.104 (0.35)	0.0442 (0.207)	0.0353 (0.177)	0.574 (0.853)	0.236 (0.549)	0.653 (0.891)	1 (1.00)
11p gain	30 (6%)	482	0.179 (0.459)	0.0295 (0.162)	0.348 (0.672)	0.181 (0.464)	0.639 (0.885)	0.0081 (0.07)	1 (1.00)	0.431 (0.77)
19q gain	25 (5%)	487	1.92e-07 (8.9e-06)	7.02e-06 (0.000228)	0.416 (0.755)	0.069 (0.274)	0.0675 (0.271)	0.155 (0.429)	0.0983 (0.337)	0.67 (0.896)
22q gain	23 (4%)	489	0.645 (0.888)	0.0457 (0.213)	0.831 (0.985)	0.121 (0.375)	0.19 (0.478)	0.00383 (0.04)	0.731 (0.94)	0.159 (0.433)
3p loss	30 (6%)	482	0.0496 (0.223)	0.883 (1.00)	0.45 (0.795)	0.243 (0.555)	0.00192 (0.024)	0.915 (1.00)	0.312 (0.633)	0.431 (0.77)
5p loss	35 (7%)	477	0.871 (1.00)	0.254 (0.571)	0.862 (1.00)	0.00747 (0.0658)	0.357 (0.686)	0.00983 (0.0767)	0.57 (0.853)	0.153 (0.427)
5q loss	32 (6%)	480	0.28 (0.595)	0.29 (0.611)	0.583 (0.857)	0.00504 (0.0496)	0.67 (0.896)	0.04 (0.196)	0.662 (0.892)	0.712 (0.924)
11q loss	21 (4%)	491	9.86e-05 (0.00213)	0.149 (0.418)	1 (1.00)	0.081 (0.304)	0.0821 (0.304)	0.0141 (0.102)	1 (1.00)	1 (1.00)
16p loss	14 (3%)	498	0.052 (0.229)	0.000244 (0.00427)	1 (1.00)	0.266 (0.581)	0.149 (0.418)	0.741 (0.945)	0.582 (0.857)	0.239 (0.553)
16q loss	22 (4%)	490	0.0745 (0.289)	0.000217 (0.0039)	0.664 (0.892)	0.0212 (0.131)	0.0737 (0.289)	0.513 (0.825)	0.491 (0.813)	0.652 (0.891)
18q loss	62 (12%)	450	0.573 (0.853)	0.0236 (0.141)	0.499 (0.816)	0.885 (1.00)	0.858 (1.00)	0.0326 (0.172)	0.104 (0.35)	0.784 (0.972)
19p loss	26 (5%)	486	0.909 (1.00)	0.677 (0.901)	0.843 (0.993)	0.3 (0.621)	0.0817 (0.304)	0.934 (1.00)	0.0219 (0.133)	0.0594 (0.247)
21q loss	38 (7%)	474	0.694 (0.917)	0.495 (0.815)	0.737 (0.944)	0.148 (0.418)	0.00752 (0.0658)	0.00412 (0.0424)	0.586 (0.857)	1 (1.00)
1q gain	23 (4%)	489	0.457 (0.8)	5.1e-05 (0.00122)	0.522 (0.831)	0.655 (0.891)	0.112 (0.364)	0.0831 (0.306)	0.276 (0.59)	0.385 (0.722)
4q gain	7 (1%)	505	0.11 (0.364)	0.0109 (0.084)	0.47 (0.804)	0.259 (0.576)		0.157 (0.432)	1 (1.00)	1 (1.00)
8q gain	55 (11%)	457	0.719 (0.932)	0.23 (0.549)	0.774 (0.969)	0.0159 (0.106)	0.335 (0.661)	0.176 (0.457)	0.63 (0.885)	0.369 (0.707)
10q gain	11 (2%)	501	0.856 (1.00)	0.24 (0.553)	1 (1.00)	0.543 (0.848)	0.336 (0.661)	0.0087 (0.0723)	0.0933 (0.328)	0.14 (0.409)
12p gain	32 (6%)	480	0.301 (0.621)	0.462 (0.8)	0.273 (0.589)	0.0336 (0.173)	0.832 (0.985)	0.471 (0.804)	0.345 (0.669)	0.711 (0.924)
12q gain	15 (3%)	497	0.00551 (0.0525)	0.324 (0.648)	0.193 (0.481)	0.581 (0.857)	0.12 (0.375)	0.8 (0.973)	0.154 (0.427)	0.613 (0.875)
13q gain	6 (1%)	506	0.41 (0.753)	0.94 (1.00)	1 (1.00)	0.0332 (0.172)	0.0678 (0.271)	1 (1.00)	1 (1.00)	1 (1.00)
16p gain	16 (3%)	496	0.616 (0.877)	0.0319 (0.17)	0.445 (0.787)	0.426 (0.767)	0.708 (0.924)	0.146 (0.418)	0.609 (0.875)	0.613 (0.875)
16q gain	19 (4%)	493	0.417 (0.755)	0.606 (0.875)	0.49 (0.813)	0.461 (0.8)	0.638 (0.885)	0.0153 (0.106)	0.677 (0.901)	0.623 (0.88)
17q gain	23 (4%)	489	0.00836 (0.0713)	0.118 (0.374)	0.0858 (0.312)	0.663 (0.892)	0.961 (1.00)	0.27 (0.586)	0.26 (0.577)	0.636 (0.885)
18p gain	18 (4%)	494	0.0174 (0.112)	0.906 (1.00)	0.639 (0.885)	0.806 (0.973)	0.383 (0.722)	0.564 (0.849)	0.306 (0.626)	0.619 (0.879)
18q gain	13 (3%)	499	0.000572 (0.00883)	0.781 (0.972)	1 (1.00)	0.145 (0.418)	0.507 (0.819)	0.46 (0.8)	0.192 (0.481)	1 (1.00)
21q gain	23 (4%)	489	0.276 (0.59)	0.00537 (0.0519)	0.285 (0.603)	0.177 (0.457)	0.0995 (0.339)	0.829 (0.985)	0.391 (0.724)	0.389 (0.722)
xp gain	22 (4%)	490	0.54 (0.848)	0.897 (1.00)	0.19 (0.478)	0.177 (0.457)	0.502 (0.817)	0.0197 (0.123)	0.278 (0.593)	1 (1.00)
1q loss	26 (5%)	486	0.42 (0.759)	0.113 (0.364)	1 (1.00)	0.83 (0.985)	0.609 (0.875)	0.00319 (0.0345)	0.229 (0.549)	1 (1.00)
2p loss	21 (4%)	491	0.307 (0.627)	0.528 (0.837)	0.656 (0.891)	0.0138 (0.101)	0.0677 (0.271)	0.232 (0.549)	1 (1.00)	0.385 (0.722)
2q loss	18 (4%)	494	0.909 (1.00)	0.48 (0.813)	0.81 (0.973)	0.121 (0.375)	0.223 (0.54)	0.0488 (0.221)	1 (1.00)	0.623 (0.88)
3q loss	28 (5%)	484	0.0258 (0.15)	0.443 (0.787)	0.697 (0.917)	0.3 (0.621)	0.0955 (0.332)	0.97 (1.00)	0.276 (0.59)	0.7 (0.92)
4q loss	94 (18%)	418	0.471 (0.804)	0.38 (0.722)	0.207 (0.509)	0.809 (0.973)	0.745 (0.948)	0.0158 (0.106)	0.823 (0.983)	0.816 (0.977)
8p loss	17 (3%)	495	0.0474 (0.218)	0.174 (0.457)	0.81 (0.973)	0.0912 (0.325)	0.327 (0.65)	0.386 (0.722)	0.113 (0.364)	0.317 (0.638)
8q loss	11 (2%)	501	0.0439 (0.207)	0.111 (0.364)	0.551 (0.849)	0.163 (0.442)	0.507 (0.819)	0.798 (0.973)	0.0936 (0.328)	0.164 (0.442)
12q loss	52 (10%)	460	0.748 (0.951)	0.177 (0.457)	0.77 (0.967)	0.125 (0.382)	0.795 (0.973)	0.00291 (0.032)	0.791 (0.973)	0.233 (0.549)
13q loss	115 (22%)	397	0.248 (0.564)	0.721 (0.933)	0.136 (0.403)	0.000328 (0.00545)	0.137 (0.403)	0.509 (0.82)	0.294 (0.615)	0.388 (0.722)
18p loss	67 (13%)	445	0.613 (0.875)	0.00237 (0.0273)	0.147 (0.418)	1 (1.00)	0.458 (0.8)	0.184 (0.468)	0.097 (0.335)	0.784 (0.972)
20p loss	7 (1%)	505	0.904 (1.00)	0.858 (1.00)	0.251 (0.566)	0.0472 (0.218)	0.43 (0.77)	0.495 (0.815)	0.147 (0.418)	0.386 (0.722)
xq loss	70 (14%)	442	0.00654 (0.0589)	0.149 (0.418)	0.607 (0.875)	0.0959 (0.332)	0.157 (0.432)	0.707 (0.924)	0.651 (0.891)	1 (1.00)
2p gain	14 (3%)	498	0.149 (0.418)	0.0783 (0.3)	0.787 (0.972)	0.387 (0.722)	0.485 (0.813)	0.548 (0.849)	1 (1.00)	0.599 (0.872)
2q gain	13 (3%)	499	0.321 (0.645)	0.172 (0.457)	0.577 (0.856)	0.142 (0.414)	0.485 (0.813)	0.559 (0.849)	1 (1.00)	0.569 (0.853)
4p gain	12 (2%)	500	0.903 (1.00)	0.122 (0.376)	1 (1.00)	0.386 (0.722)	0.695 (0.917)	0.0813 (0.304)	0.168 (0.45)	1 (1.00)
6p gain	7 (1%)	505	0.539 (0.848)	0.123 (0.377)	0.251 (0.566)	0.0867 (0.314)	0.824 (0.983)	0.235 (0.549)	1 (1.00)	1 (1.00)
8p gain	45 (9%)	467	0.62 (0.879)	0.867 (1.00)	0.638 (0.885)	0.073 (0.288)	0.127 (0.386)	0.299 (0.621)	0.552 (0.849)	0.753 (0.955)
11q gain	58 (11%)	454	0.129 (0.388)	0.122 (0.376)	0.263 (0.578)	0.886 (1.00)	0.807 (0.973)	0.235 (0.549)	0.901 (1.00)	0.767 (0.966)
14q gain	4 (1%)	508	0.333 (0.66)	0.252 (0.567)	1 (1.00)	0.64 (0.885)	0.978 (1.00)	0.839 (0.991)	1 (1.00)	0.243 (0.555)
7p loss	3 (1%)	509	0.73 (0.94)	0.643 (0.887)	0.588 (0.858)	0.526 (0.835)		0.787 (0.972)	1 (1.00)	1 (1.00)
7q loss	4 (1%)	508	0.884 (1.00)	0.889 (1.00)	0.633 (0.885)	0.289 (0.61)	0.49 (0.813)	0.456 (0.8)	1 (1.00)	1 (1.00)
12p loss	28 (5%)	484	0.855 (1.00)	0.111 (0.364)	0.563 (0.849)	0.417 (0.755)	0.486 (0.813)	0.136 (0.403)	1 (1.00)	1 (1.00)
15q loss	51 (10%)	461	0.313 (0.633)	0.342 (0.668)	0.658 (0.892)	0.269 (0.584)	0.774 (0.969)	0.647 (0.888)	0.784 (0.972)	0.759 (0.957)
17q loss	9 (2%)	503	0.572 (0.853)	0.081 (0.304)	0.521 (0.831)	1 (1.00)	0.119 (0.375)	0.759 (0.957)	1 (1.00)	0.116 (0.372)
20q loss	3 (1%)	509	0.926 (1.00)	0.966 (1.00)	0.0877 (0.316)	1 (1.00)	0.325 (0.648)	0.47 (0.804)	1 (1.00)	0.188 (0.476)
xp loss	98 (19%)	414	0.392 (0.724)	0.725 (0.936)	0.498 (0.816)	0.115 (0.369)	0.306 (0.626)	0.711 (0.924)	0.688 (0.911)	0.103 (0.349)

'1p gain' versus 'Time to Death'

P value = 0.016 (logrank test), Q value = 0.11

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

	nPatients	nDeath	Duration Range (Median), Month
ALL	508	125	0.0 - 211.2 (22.4)
1P GAIN MUTATED	13	6	0.2 - 51.9 (19.9)
1P GAIN WILD-TYPE	495	119	0.0 - 211.2 (22.4)

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

'1p gain' versus 'YEARS_TO_BIRTH'

P value = 0.0126 (Wilcoxon-test), Q value = 0.095

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

	nPatients	Mean (Std.Dev)
ALL	511	43.0 (13.3)
1P GAIN MUTATED	13	52.4 (12.7)
1P GAIN WILD-TYPE	498	42.7 (13.3)

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

'1p gain' versus 'RADIATION_THERAPY'

P value = 0.0344 (Fisher's exact test), Q value = 0.18

Table S3. Gene #1: '1p gain' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	184	295
1P GAIN MUTATED	1	11
1P GAIN WILD-TYPE	183	284

Figure S3. Get High-res Image Gene #1: '1p gain' versus Clinical Feature #4: 'RADIATION_THERAPY'

'1p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00907 (Fisher's exact test), Q value = 0.074

Table S4. Gene #1: '1p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	194	129	189
1P GAIN MUTATED	10	0	3
1P GAIN WILD-TYPE	184	129	186

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

'1q gain' versus 'YEARS_TO_BIRTH'

P value = 5.1e-05 (Wilcoxon-test), Q value = 0.0012

Table S5. Gene #2: '1q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	511	43.0 (13.3)
1Q GAIN MUTATED	23	54.0 (11.1)
1Q GAIN WILD-TYPE	488	42.5 (13.2)

Figure S5. Get High-res Image Gene #2: '1q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'3p gain' versus 'Time to Death'

P value = 0.039 (logrank test), Q value = 0.19

Table S6. Gene #5: '3p gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	508	125	0.0 - 211.2 (22.4)
3P GAIN MUTATED	11	4	0.2 - 49.9 (17.3)
3P GAIN WILD-TYPE	497	121	0.0 - 211.2 (22.6)

Figure S6. Get High-res Image Gene #5: '3p gain' versus Clinical Feature #1: 'Time to Death'

'3p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0288 (Fisher's exact test), Q value = 0.16

Table S7. Gene #5: '3p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	194	129	189
3P GAIN MUTATED	8	0	3
3P GAIN WILD-TYPE	186	129	186

Figure S7. Get High-res Image Gene #5: '3p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'3q gain' versus 'Time to Death'

P value = 0.0022 (logrank test), Q value = 0.026

Table S8. Gene #6: '3q gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	508	125	0.0 - 211.2 (22.4)
3Q GAIN MUTATED	8	4	0.2 - 47.8 (13.1)
3Q GAIN WILD-TYPE	500	121	0.0 - 211.2 (22.5)

Figure S8. Get High-res Image Gene #6: '3q gain' versus Clinical Feature #1: 'Time to Death'

'3q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0332 (Wilcoxon-test), Q value = 0.17

Table S9. Gene #6: '3q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	511	43.0 (13.3)
3Q GAIN MUTATED	8	52.8 (11.4)
3Q GAIN WILD-TYPE	503	42.8 (13.3)

Figure S9. Get High-res Image Gene #6: '3q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'4q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0109 (Wilcoxon-test), Q value = 0.084

Table S10. Gene #8: '4q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	511	43.0 (13.3)
4Q GAIN MUTATED	7	57.0 (15.2)
4Q GAIN WILD-TYPE	504	42.8 (13.2)

Figure S10. Get High-res Image Gene #8: '4q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'5p gain' versus 'Time to Death'

P value = 0.0305 (logrank test), Q value = 0.17

Table S11. Gene #9: '5p gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	508	125	0.0 - 211.2 (22.4)
5P GAIN MUTATED	11	6	2.5 - 62.2 (24.4)
5P GAIN WILD-TYPE	497	119	0.0 - 211.2 (22.3)

Figure S11. Get High-res Image Gene #9: '5p gain' versus Clinical Feature #1: 'Time to Death'

'5p gain' versus 'YEARS_TO_BIRTH'

P value = 0.0321 (Wilcoxon-test), Q value = 0.17

Table S12. Gene #9: '5p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	511	43.0 (13.3)
5P GAIN MUTATED	11	51.5 (12.3)
5P GAIN WILD-TYPE	500	42.8 (13.3)

Figure S12. Get High-res Image Gene #9: '5p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'5q gain' versus 'Time to Death'

P value = 0.042 (logrank test), Q value = 0.2

Table S13. Gene #10: '5q gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	508	125	0.0 - 211.2 (22.4)
5Q GAIN MUTATED	9	5	2.5 - 62.2 (24.4)
5Q GAIN WILD-TYPE	499	120	0.0 - 211.2 (22.3)

Figure S13. Get High-res Image Gene #10: '5q gain' versus Clinical Feature #1: 'Time to Death'

'5q gain' versus 'RACE'

P value = 0.0548 (Fisher's exact test), Q value = 0.24

Table S14. Gene #10: '5q gain' versus Clinical Feature #7: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	1	8	21	472
5Q GAIN MUTATED	0	1	1	6
5Q GAIN WILD-TYPE	1	7	20	466

Figure S14. Get High-res Image Gene #10: '5q gain' versus Clinical Feature #7: 'RACE'

'7p gain' versus 'Time to Death'

P value = 9.05e-08 (logrank test), Q value = 4.9e-06

Table S15. Gene #12: '7p gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	508	125	0.0 - 211.2 (22.4)
7P GAIN MUTATED	120	48	0.1 - 211.2 (18.9)
7P GAIN WILD-TYPE	388	77	0.0 - 182.3 (24.8)

Figure S15. Get High-res Image Gene #12: '7p gain' versus Clinical Feature #1: 'Time to Death'

'7p gain' versus 'YEARS_TO_BIRTH'

P value = 1.63e-10 (Wilcoxon-test), Q value = 1.8e-08

Table S16. Gene #12: '7p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	511	43.0 (13.3)
7P GAIN MUTATED	120	49.8 (12.8)
7P GAIN WILD-TYPE	391	40.9 (12.8)

Figure S16. Get High-res Image Gene #12: '7p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'7p gain' versus 'RADIATION_THERAPY'

P value = 0.000773 (Fisher's exact test), Q value = 0.011

Table S17. Gene #12: '7p gain' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	184	295
7P GAIN MUTATED	27	82
7P GAIN WILD-TYPE	157	213

Figure S17. Get High-res Image Gene #12: '7p gain' versus Clinical Feature #4: 'RADIATION_THERAPY'

'7p gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.000962 (Wilcoxon-test), Q value = 0.013

Table S18. Gene #12: '7p gain' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	306	86.7 (12.6)
7P GAIN MUTATED	74	81.9 (15.3)
7P GAIN WILD-TYPE	232	88.2 (11.2)

Figure S18. Get High-res Image Gene #12: '7p gain' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'7p gain' versus 'RACE'

P value = 0.0159 (Fisher's exact test), Q value = 0.11

Table S19. Gene #12: '7p gain' versus Clinical Feature #7: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	1	8	21	472
7P GAIN MUTATED	1	2	10	107
7P GAIN WILD-TYPE	0	6	11	365

Figure S19. Get High-res Image Gene #12: '7p gain' versus Clinical Feature #7: 'RACE'

'7q gain' versus 'Time to Death'

P value = 2.81e-07 (logrank test), Q value = 1.2e-05

Table S20. Gene #13: '7q gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	508	125	0.0 - 211.2 (22.4)
7Q GAIN MUTATED	150	57	0.1 - 211.2 (19.2)
7Q GAIN WILD-TYPE	358	68	0.0 - 182.3 (24.4)

Figure S20. Get High-res Image Gene #13: '7q gain' versus Clinical Feature #1: 'Time to Death'

'7q gain' versus 'YEARS_TO_BIRTH'

P value = 1.96e-10 (Wilcoxon-test), Q value = 1.8e-08

Table S21. Gene #13: '7q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	511	43.0 (13.3)
7Q GAIN MUTATED	150	48.8 (13.1)
7Q GAIN WILD-TYPE	361	40.6 (12.7)

Figure S21. Get High-res Image Gene #13: '7q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'7q gain' versus 'RADIATION_THERAPY'

P value = 0.00116 (Fisher's exact test), Q value = 0.015

Table S22. Gene #13: '7q gain' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	184	295
7Q GAIN MUTATED	36	99
7Q GAIN WILD-TYPE	148	196

Figure S22. Get High-res Image Gene #13: '7q gain' versus Clinical Feature #4: 'RADIATION_THERAPY'

'7q gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00576 (Wilcoxon-test), Q value = 0.054

Table S23. Gene #13: '7q gain' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	306	86.7 (12.6)
7Q GAIN MUTATED	89	83.1 (14.6)
7Q GAIN WILD-TYPE	217	88.1 (11.4)

Figure S23. Get High-res Image Gene #13: '7q gain' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'7q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0514 (Fisher's exact test), Q value = 0.23

Table S24. Gene #13: '7q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	194	129	189
7Q GAIN MUTATED	67	39	44
7Q GAIN WILD-TYPE	127	90	145

Figure S24. Get High-res Image Gene #13: '7q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'7q gain' versus 'RACE'

P value = 0.00939 (Fisher's exact test), Q value = 0.076

Table S25. Gene #13: '7q gain' versus Clinical Feature #7: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	1	8	21	472
7Q GAIN MUTATED	1	3	12	134
7Q GAIN WILD-TYPE	0	5	9	338

Figure S25. Get High-res Image Gene #13: '7q gain' versus Clinical Feature #7: 'RACE'

'8q gain' versus 'RADIATION_THERAPY'

P value = 0.0159 (Fisher's exact test), Q value = 0.11

Table S26. Gene #15: '8q gain' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	184	295
8Q GAIN MUTATED	12	40
8Q GAIN WILD-TYPE	172	255

Figure S26. Get High-res Image Gene #15: '8q gain' versus Clinical Feature #4: 'RADIATION_THERAPY'

'9p gain' versus 'GENDER'

P value = 0.0442 (Fisher's exact test), Q value = 0.21

Table S27. Gene #16: '9p gain' versus Clinical Feature #3: 'GENDER'

nPatients	FEMALE	MALE
ALL	228	284
9P GAIN MUTATED	12	5
9P GAIN WILD-TYPE	216	279

Figure S27. Get High-res Image Gene #16: '9p gain' versus Clinical Feature #3: 'GENDER'

'9p gain' versus 'RADIATION_THERAPY'

P value = 0.0353 (Fisher's exact test), Q value = 0.18

Table S28. Gene #16: '9p gain' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	184	295
9P GAIN MUTATED	2	14
9P GAIN WILD-TYPE	182	281

Figure S28. Get High-res Image Gene #16: '9p gain' versus Clinical Feature #4: 'RADIATION_THERAPY'

'9q gain' versus 'GENDER'

P value = 0.00268 (Fisher's exact test), Q value = 0.03

Table S29. Gene #17: '9q gain' versus Clinical Feature #3: 'GENDER'

nPatients	FEMALE	MALE
ALL	228	284
9Q GAIN MUTATED	18	6
9Q GAIN WILD-TYPE	210	278

Figure S29. Get High-res Image Gene #17: '9q gain' versus Clinical Feature #3: 'GENDER'

'9q gain' versus 'RADIATION_THERAPY'

P value = 0.00177 (Fisher's exact test), Q value = 0.023

Table S30. Gene #17: '9q gain' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	184	295
9Q GAIN MUTATED	2	21
9Q GAIN WILD-TYPE	182	274

Figure S30. Get High-res Image Gene #17: '9q gain' versus Clinical Feature #4: 'RADIATION_THERAPY'

'9q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0586 (Fisher's exact test), Q value = 0.25

Table S31. Gene #17: '9q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	194	129	189
9Q GAIN MUTATED	14	6	4
9Q GAIN WILD-TYPE	180	123	185

Figure S31. Get High-res Image Gene #17: '9q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'10p gain' versus 'YEARS_TO_BIRTH'

P value = 0.0215 (Wilcoxon-test), Q value = 0.13

Table S32. Gene #18: '10p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	511	43.0 (13.3)
10P GAIN MUTATED	57	38.5 (10.9)
10P GAIN WILD-TYPE	454	43.6 (13.5)

Figure S32. Get High-res Image Gene #18: '10p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'10p gain' versus 'RADIATION_THERAPY'

P value = 0.0159 (Fisher's exact test), Q value = 0.11

Table S33. Gene #18: '10p gain' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	184	295
10P GAIN MUTATED	12	41
10P GAIN WILD-TYPE	172	254

Figure S33. Get High-res Image Gene #18: '10p gain' versus Clinical Feature #4: 'RADIATION_THERAPY'

'10p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00026 (Fisher's exact test), Q value = 0.0044

Table S34. Gene #18: '10p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	194	129	189
10P GAIN MUTATED	32	17	8
10P GAIN WILD-TYPE	162	112	181

Figure S34. Get High-res Image Gene #18: '10p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'10q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0087 (Fisher's exact test), Q value = 0.072

Table S35. Gene #19: '10q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	194	129	189
10Q GAIN MUTATED	9	0	2
10Q GAIN WILD-TYPE	185	129	187

Figure S35. Get High-res Image Gene #19: '10q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'11p gain' versus 'YEARS_TO_BIRTH'

P value = 0.0295 (Wilcoxon-test), Q value = 0.16

Table S36. Gene #20: '11p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	511	43.0 (13.3)
11P GAIN MUTATED	30	48.8 (14.9)
11P GAIN WILD-TYPE	481	42.6 (13.2)

Figure S36. Get High-res Image Gene #20: '11p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'11p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0081 (Fisher's exact test), Q value = 0.07

Table S37. Gene #20: '11p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	194	129	189
11P GAIN MUTATED	4	9	17
11P GAIN WILD-TYPE	190	120	172

Figure S37. Get High-res Image Gene #20: '11p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'12p gain' versus 'RADIATION_THERAPY'

P value = 0.0336 (Fisher's exact test), Q value = 0.17

Table S38. Gene #22: '12p gain' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	184	295
12P GAIN MUTATED	6	24
12P GAIN WILD-TYPE	178	271

Figure S38. Get High-res Image Gene #22: '12p gain' versus Clinical Feature #4: 'RADIATION_THERAPY'

'12q gain' versus 'Time to Death'

P value = 0.00551 (logrank test), Q value = 0.053

Table S39. Gene #23: '12q gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	508	125	0.0 - 211.2 (22.4)
12Q GAIN MUTATED	15	9	1.2 - 84.3 (30.2)
12Q GAIN WILD-TYPE	493	116	0.0 - 211.2 (22.1)

Figure S39. Get High-res Image Gene #23: '12q gain' versus Clinical Feature #1: 'Time to Death'

'13q gain' versus 'RADIATION_THERAPY'

P value = 0.0332 (Fisher's exact test), Q value = 0.17

Table S40. Gene #24: '13q gain' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	184	295
13Q GAIN MUTATED	5	1
13Q GAIN WILD-TYPE	179	294

Figure S40. Get High-res Image Gene #24: '13q gain' versus Clinical Feature #4: 'RADIATION_THERAPY'

'15q gain' versus 'Time to Death'

P value = 0.0166 (logrank test), Q value = 0.11

Table S41. Gene #26: '15q gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	508	125	0.0 - 211.2 (22.4)
15Q GAIN MUTATED	11	7	2.4 - 117.4 (32.5)
15Q GAIN WILD-TYPE	497	118	0.0 - 211.2 (22.3)

Figure S41. Get High-res Image Gene #26: '15q gain' versus Clinical Feature #1: 'Time to Death'

'15q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0259 (Wilcoxon-test), Q value = 0.15

Table S42. Gene #26: '15q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	511	43.0 (13.3)
15Q GAIN MUTATED	11	51.8 (13.3)
15Q GAIN WILD-TYPE	500	42.8 (13.3)

Figure S42. Get High-res Image Gene #26: '15q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'15q gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0135 (Wilcoxon-test), Q value = 0.1

Table S43. Gene #26: '15q gain' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	306	86.7 (12.6)
15Q GAIN MUTATED	10	72.0 (19.9)
15Q GAIN WILD-TYPE	296	87.2 (12.0)

Figure S43. Get High-res Image Gene #26: '15q gain' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'16p gain' versus 'YEARS_TO_BIRTH'

P value = 0.0319 (Wilcoxon-test), Q value = 0.17

Table S44. Gene #27: '16p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	511	43.0 (13.3)
16P GAIN MUTATED	16	49.8 (11.8)
16P GAIN WILD-TYPE	495	42.8 (13.3)

Figure S44. Get High-res Image Gene #27: '16p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'16q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0153 (Fisher's exact test), Q value = 0.11

Table S45. Gene #28: '16q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	194	129	189
16Q GAIN MUTATED	13	1	5
16Q GAIN WILD-TYPE	181	128	184

Figure S45. Get High-res Image Gene #28: '16q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'17p gain' versus 'Time to Death'

P value = 0.0143 (logrank test), Q value = 0.1

Table S46. Gene #29: '17p gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	508	125	0.0 - 211.2 (22.4)
17P GAIN MUTATED	20	8	8.1 - 62.2 (21.6)
17P GAIN WILD-TYPE	488	117	0.0 - 211.2 (22.5)

Figure S46. Get High-res Image Gene #29: '17p gain' versus Clinical Feature #1: 'Time to Death'

'17p gain' versus 'YEARS_TO_BIRTH'

P value = 0.0176 (Wilcoxon-test), Q value = 0.11

Table S47. Gene #29: '17p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	511	43.0 (13.3)
17P GAIN MUTATED	20	49.9 (13.4)
17P GAIN WILD-TYPE	491	42.7 (13.3)

Figure S47. Get High-res Image Gene #29: '17p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'17p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.059 (Fisher's exact test), Q value = 0.25

Table S48. Gene #29: '17p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	194	129	189
17P GAIN MUTATED	11	1	8
17P GAIN WILD-TYPE	183	128	181

Figure S48. Get High-res Image Gene #29: '17p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'17q gain' versus 'Time to Death'

P value = 0.00836 (logrank test), Q value = 0.071

Table S49. Gene #30: '17q gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	508	125	0.0 - 211.2 (22.4)
17Q GAIN MUTATED	23	9	5.8 - 62.2 (21.0)
17Q GAIN WILD-TYPE	485	116	0.0 - 211.2 (22.4)

Figure S49. Get High-res Image Gene #30: '17q gain' versus Clinical Feature #1: 'Time to Death'

'18p gain' versus 'Time to Death'

P value = 0.0174 (logrank test), Q value = 0.11

Table S50. Gene #31: '18p gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	508	125	0.0 - 211.2 (22.4)
18P GAIN MUTATED	18	9	0.2 - 117.5 (25.0)
18P GAIN WILD-TYPE	490	116	0.0 - 211.2 (22.4)

Figure S50. Get High-res Image Gene #31: '18p gain' versus Clinical Feature #1: 'Time to Death'

'18q gain' versus 'Time to Death'

P value = 0.000572 (logrank test), Q value = 0.0088

Table S51. Gene #32: '18q gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	508	125	0.0 - 211.2 (22.4)
18Q GAIN MUTATED	13	8	0.2 - 51.9 (29.1)
18Q GAIN WILD-TYPE	495	117	0.0 - 211.2 (22.3)

Figure S51. Get High-res Image Gene #32: '18q gain' versus Clinical Feature #1: 'Time to Death'

'19p gain' versus 'YEARS_TO_BIRTH'

P value = 0.00964 (Wilcoxon-test), Q value = 0.076

Table S52. Gene #33: '19p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	511	43.0 (13.3)
19P GAIN MUTATED	98	46.3 (14.2)
19P GAIN WILD-TYPE	413	42.2 (13.0)

Figure S52. Get High-res Image Gene #33: '19p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'19p gain' versus 'RADIATION_THERAPY'

P value = 0.043 (Fisher's exact test), Q value = 0.21

Table S53. Gene #33: '19p gain' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	184	295
19P GAIN MUTATED	44	48
19P GAIN WILD-TYPE	140	247

Figure S53. Get High-res Image Gene #33: '19p gain' versus Clinical Feature #4: 'RADIATION_THERAPY'

'19p gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00028

Table S54. Gene #33: '19p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	194	129	189
19P GAIN MUTATED	20	19	60
19P GAIN WILD-TYPE	174	110	129

Figure S54. Get High-res Image Gene #33: '19p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'19q gain' versus 'Time to Death'

P value = 1.92e-07 (logrank test), Q value = 8.9e-06

Table S55. Gene #34: '19q gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	508	125	0.0 - 211.2 (22.4)
19Q GAIN MUTATED	25	11	0.2 - 54.8 (16.8)
19Q GAIN WILD-TYPE	483	114	0.0 - 211.2 (23.5)

Figure S55. Get High-res Image Gene #34: '19q gain' versus Clinical Feature #1: 'Time to Death'

'19q gain' versus 'YEARS_TO_BIRTH'

P value = 7.02e-06 (Wilcoxon-test), Q value = 0.00023

Table S56. Gene #34: '19q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	511	43.0 (13.3)
19Q GAIN MUTATED	25	55.2 (11.7)
19Q GAIN WILD-TYPE	486	42.4 (13.1)

Figure S56. Get High-res Image Gene #34: '19q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'20p gain' versus 'Time to Death'

P value = 2.94e-12 (logrank test), Q value = 3.8e-10

Table S57. Gene #35: '20p gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	508	125	0.0 - 211.2 (22.4)
20P GAIN MUTATED	45	23	0.5 - 54.8 (17.7)
20P GAIN WILD-TYPE	463	102	0.0 - 211.2 (23.5)

Figure S57. Get High-res Image Gene #35: '20p gain' versus Clinical Feature #1: 'Time to Death'

'20p gain' versus 'YEARS_TO_BIRTH'

P value = 7.25e-09 (Wilcoxon-test), Q value = 5.2e-07

Table S58. Gene #35: '20p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	511	43.0 (13.3)
20P GAIN MUTATED	45	54.4 (11.8)
20P GAIN WILD-TYPE	466	41.9 (13.0)

Figure S58. Get High-res Image Gene #35: '20p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'20p gain' versus 'RADIATION_THERAPY'

P value = 0.0282 (Fisher's exact test), Q value = 0.16

Table S59. Gene #35: '20p gain' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	184	295
20P GAIN MUTATED	9	32
20P GAIN WILD-TYPE	175	263

Figure S59. Get High-res Image Gene #35: '20p gain' versus Clinical Feature #4: 'RADIATION_THERAPY'

'20p gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00967 (Wilcoxon-test), Q value = 0.076

Table S60. Gene #35: '20p gain' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	306	86.7 (12.6)
20P GAIN MUTATED	28	81.4 (13.5)
20P GAIN WILD-TYPE	278	87.2 (12.4)

Figure S60. Get High-res Image Gene #35: '20p gain' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'20q gain' versus 'Time to Death'

P value = 2.04e-09 (logrank test), Q value = 1.6e-07

Table S61. Gene #36: '20q gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	508	125	0.0 - 211.2 (22.4)
20Q GAIN MUTATED	44	22	0.5 - 117.5 (17.6)
20Q GAIN WILD-TYPE	464	103	0.0 - 211.2 (23.5)

Figure S61. Get High-res Image Gene #36: '20q gain' versus Clinical Feature #1: 'Time to Death'

'20q gain' versus 'YEARS_TO_BIRTH'

P value = 2.04e-08 (Wilcoxon-test), Q value = 1.2e-06

Table S62. Gene #36: '20q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	511	43.0 (13.3)
20Q GAIN MUTATED	44	54.3 (12.2)
20Q GAIN WILD-TYPE	467	41.9 (13.0)

Figure S62. Get High-res Image Gene #36: '20q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'20q gain' versus 'RADIATION_THERAPY'

P value = 0.0282 (Fisher's exact test), Q value = 0.16

Table S63. Gene #36: '20q gain' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	184	295
20Q GAIN MUTATED	9	32
20Q GAIN WILD-TYPE	175	263

Figure S63. Get High-res Image Gene #36: '20q gain' versus Clinical Feature #4: 'RADIATION_THERAPY'

'20q gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0145 (Wilcoxon-test), Q value = 0.1

Table S64. Gene #36: '20q gain' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	306	86.7 (12.6)
20Q GAIN MUTATED	27	81.5 (13.8)
20Q GAIN WILD-TYPE	279	87.2 (12.4)

Figure S64. Get High-res Image Gene #36: '20q gain' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'21q gain' versus 'YEARS_TO_BIRTH'

P value = 0.00537 (Wilcoxon-test), Q value = 0.052

Table S65. Gene #37: '21q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	511	43.0 (13.3)
21Q GAIN MUTATED	23	52.5 (17.3)
21Q GAIN WILD-TYPE	488	42.5 (13.0)

Figure S65. Get High-res Image Gene #37: '21q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'22q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0457 (Wilcoxon-test), Q value = 0.21

Table S66. Gene #38: '22q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	511	43.0 (13.3)
22Q GAIN MUTATED	23	48.0 (11.3)
22Q GAIN WILD-TYPE	488	42.8 (13.4)

Figure S66. Get High-res Image Gene #38: '22q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'22q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00383 (Fisher's exact test), Q value = 0.04

Table S67. Gene #38: '22q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	194	129	189
22Q GAIN MUTATED	3	4	16
22Q GAIN WILD-TYPE	191	125	173

Figure S67. Get High-res Image Gene #38: '22q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'xp gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0197 (Fisher's exact test), Q value = 0.12

Table S68. Gene #39: 'xp gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	194	129	189
XP GAIN MUTATED	14	5	3
XP GAIN WILD-TYPE	180	124	186

Figure S68. Get High-res Image Gene #39: 'xp gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'xq gain' versus 'YEARS_TO_BIRTH'

P value = 0.0539 (Wilcoxon-test), Q value = 0.24

Table S69. Gene #40: 'xq gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	511	43.0 (13.3)
XQ GAIN MUTATED	41	39.5 (12.1)
XQ GAIN WILD-TYPE	470	43.3 (13.4)

Figure S69. Get High-res Image Gene #40: 'xq gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'xq gain' versus 'GENDER'

P value = 0.0136 (Fisher's exact test), Q value = 0.1

Table S70. Gene #40: 'xq gain' versus Clinical Feature #3: 'GENDER'

nPatients	FEMALE	MALE
ALL	228	284
XQ GAIN MUTATED	26	15
XQ GAIN WILD-TYPE	202	269

Figure S70. Get High-res Image Gene #40: 'xq gain' versus Clinical Feature #3: 'GENDER'

'xq gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00437 (Fisher's exact test), Q value = 0.044

Table S71. Gene #40: 'xq gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	194	129	189
XQ GAIN MUTATED	20	15	6
XQ GAIN WILD-TYPE	174	114	183

Figure S71. Get High-res Image Gene #40: 'xq gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'xq gain' versus 'ETHNICITY'

P value = 0.0254 (Fisher's exact test), Q value = 0.15

Table S72. Gene #40: 'xq gain' versus Clinical Feature #8: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	32	446
XQ GAIN MUTATED	6	30
XQ GAIN WILD-TYPE	26	416

Figure S72. Get High-res Image Gene #40: 'xq gain' versus Clinical Feature #8: 'ETHNICITY'

'1p loss' versus 'Time to Death'

P value = 0.000112 (logrank test), Q value = 0.0022

Table S73. Gene #41: '1p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	508	125	0.0 - 211.2 (22.4)
1P LOSS MUTATED	181	27	0.1 - 182.3 (23.2)
1P LOSS WILD-TYPE	327	98	0.0 - 211.2 (21.3)

Figure S73. Get High-res Image Gene #41: '1p loss' versus Clinical Feature #1: 'Time to Death'

'1p loss' versus 'YEARS_TO_BIRTH'

P value = 0.000914 (Wilcoxon-test), Q value = 0.013

Table S74. Gene #41: '1p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	511	43.0 (13.3)
1P LOSS MUTATED	183	45.4 (12.8)
1P LOSS WILD-TYPE	328	41.6 (13.5)

Figure S74. Get High-res Image Gene #41: '1p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'1p loss' versus 'RADIATION_THERAPY'

P value = 1.83e-07 (Fisher's exact test), Q value = 8.9e-06

Table S75. Gene #41: '1p loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	184	295
1P LOSS MUTATED	93	79
1P LOSS WILD-TYPE	91	216

Figure S75. Get High-res Image Gene #41: '1p loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

'1p loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00028

Table S76. Gene #41: '1p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	194	129	189
1P LOSS MUTATED	10	38	136
1P LOSS WILD-TYPE	184	91	53

Figure S76. Get High-res Image Gene #41: '1p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'1q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00319 (Fisher's exact test), Q value = 0.034

Table S77. Gene #42: '1q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	194	129	189
1Q LOSS MUTATED	4	4	18
1Q LOSS WILD-TYPE	190	125	171

Figure S77. Get High-res Image Gene #42: '1q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'2p loss' versus 'RADIATION_THERAPY'

P value = 0.0138 (Fisher's exact test), Q value = 0.1

Table S78. Gene #43: '2p loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	184	295
2P LOSS MUTATED	2	17
2P LOSS WILD-TYPE	182	278

Figure S78. Get High-res Image Gene #43: '2p loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

'2q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0488 (Fisher's exact test), Q value = 0.22

Table S79. Gene #44: '2q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	194	129	189
2Q LOSS MUTATED	12	3	3
2Q LOSS WILD-TYPE	182	126	186

Figure S79. Get High-res Image Gene #44: '2q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'3p loss' versus 'Time to Death'

P value = 0.0496 (logrank test), Q value = 0.22

Table S80. Gene #45: '3p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	508	125	0.0 - 211.2 (22.4)
3P LOSS MUTATED	29	11	0.1 - 84.3 (24.3)
3P LOSS WILD-TYPE	479	114	0.0 - 211.2 (22.3)

Figure S80. Get High-res Image Gene #45: '3p loss' versus Clinical Feature #1: 'Time to Death'

'3p loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00192 (Wilcoxon-test), Q value = 0.024

Table S81. Gene #45: '3p loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	306	86.7 (12.6)
3P LOSS MUTATED	21	78.6 (13.9)
3P LOSS WILD-TYPE	285	87.3 (12.3)

Figure S81. Get High-res Image Gene #45: '3p loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'3q loss' versus 'Time to Death'

P value = 0.0258 (logrank test), Q value = 0.15

Table S82. Gene #46: '3q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	508	125	0.0 - 211.2 (22.4)
3Q LOSS MUTATED	28	13	0.0 - 117.4 (24.2)
3Q LOSS WILD-TYPE	480	112	0.1 - 211.2 (22.3)

Figure S82. Get High-res Image Gene #46: '3q loss' versus Clinical Feature #1: 'Time to Death'

'4p loss' versus 'YEARS_TO_BIRTH'

P value = 0.0188 (Wilcoxon-test), Q value = 0.12

Table S83. Gene #47: '4p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	511	43.0 (13.3)
4P LOSS MUTATED	72	46.3 (12.8)
4P LOSS WILD-TYPE	439	42.5 (13.4)

Figure S83. Get High-res Image Gene #47: '4p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'4p loss' versus 'GENDER'

P value = 0.0413 (Fisher's exact test), Q value = 0.2

Table S84. Gene #47: '4p loss' versus Clinical Feature #3: 'GENDER'

nPatients	FEMALE	MALE
ALL	228	284
4P LOSS MUTATED	24	48
4P LOSS WILD-TYPE	204	236

Figure S84. Get High-res Image Gene #47: '4p loss' versus Clinical Feature #3: 'GENDER'

'4p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00049 (Fisher's exact test), Q value = 0.0077

Table S85. Gene #47: '4p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	194	129	189
4P LOSS MUTATED	14	19	39
4P LOSS WILD-TYPE	180	110	150

Figure S85. Get High-res Image Gene #47: '4p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'4q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0158 (Fisher's exact test), Q value = 0.11

Table S86. Gene #48: '4q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	194	129	189
4Q LOSS MUTATED	25	23	46
4Q LOSS WILD-TYPE	169	106	143

Figure S86. Get High-res Image Gene #48: '4q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'5p loss' versus 'RADIATION_THERAPY'

P value = 0.00747 (Fisher's exact test), Q value = 0.066

Table S87. Gene #49: '5p loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	184	295
5P LOSS MUTATED	5	27
5P LOSS WILD-TYPE	179	268

Figure S87. Get High-res Image Gene #49: '5p loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

'5p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00983 (Fisher's exact test), Q value = 0.077

Table S88. Gene #49: '5p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	194	129	189
5P LOSS MUTATED	19	11	5
5P LOSS WILD-TYPE	175	118	184

Figure S88. Get High-res Image Gene #49: '5p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'5q loss' versus 'RADIATION_THERAPY'

P value = 0.00504 (Fisher's exact test), Q value = 0.05

Table S89. Gene #50: '5q loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	184	295
5Q LOSS MUTATED	4	25
5Q LOSS WILD-TYPE	180	270

Figure S89. Get High-res Image Gene #50: '5q loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

'5q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.04 (Fisher's exact test), Q value = 0.2

Table S90. Gene #50: '5q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	194	129	189
5Q LOSS MUTATED	19	6	7
5Q LOSS WILD-TYPE	175	123	182

Figure S90. Get High-res Image Gene #50: '5q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'6p loss' versus 'Time to Death'

P value = 0.000108 (logrank test), Q value = 0.0022

Table S91. Gene #51: '6p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	508	125	0.0 - 211.2 (22.4)
6P LOSS MUTATED	30	13	0.2 - 65.4 (19.3)
6P LOSS WILD-TYPE	478	112	0.0 - 211.2 (22.5)

Figure S91. Get High-res Image Gene #51: '6p loss' versus Clinical Feature #1: 'Time to Death'

'6p loss' versus 'YEARS_TO_BIRTH'

P value = 0.0548 (Wilcoxon-test), Q value = 0.24

Table S92. Gene #51: '6p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	511	43.0 (13.3)
6P LOSS MUTATED	30	47.7 (14.7)
6P LOSS WILD-TYPE	481	42.7 (13.2)

Figure S92. Get High-res Image Gene #51: '6p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'6p loss' versus 'RADIATION_THERAPY'

P value = 0.0583 (Fisher's exact test), Q value = 0.25

Table S93. Gene #51: '6p loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	184	295
6P LOSS MUTATED	5	20
6P LOSS WILD-TYPE	179	275

Figure S93. Get High-res Image Gene #51: '6p loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

'6q loss' versus 'Time to Death'

P value = 7.35e-05 (logrank test), Q value = 0.0017

Table S94. Gene #52: '6q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	508	125	0.0 - 211.2 (22.4)
6Q LOSS MUTATED	61	20	0.1 - 65.4 (18.0)
6Q LOSS WILD-TYPE	447	105	0.0 - 211.2 (23.6)

Figure S94. Get High-res Image Gene #52: '6q loss' versus Clinical Feature #1: 'Time to Death'

'6q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0291 (Wilcoxon-test), Q value = 0.16

Table S95. Gene #52: '6q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	511	43.0 (13.3)
6Q LOSS MUTATED	62	46.4 (13.7)
6Q LOSS WILD-TYPE	449	42.5 (13.2)

Figure S95. Get High-res Image Gene #52: '6q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'6q loss' versus 'RADIATION_THERAPY'

P value = 0.0253 (Fisher's exact test), Q value = 0.15

Table S96. Gene #52: '6q loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	184	295
6Q LOSS MUTATED	13	41
6Q LOSS WILD-TYPE	171	254

Figure S96. Get High-res Image Gene #52: '6q loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

'6q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00121 (Wilcoxon-test), Q value = 0.016

Table S97. Gene #52: '6q loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	306	86.7 (12.6)
6Q LOSS MUTATED	40	81.0 (13.2)
6Q LOSS WILD-TYPE	266	87.5 (12.3)

Figure S97. Get High-res Image Gene #52: '6q loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'6q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00115 (Fisher's exact test), Q value = 0.015

Table S98. Gene #52: '6q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	194	129	189
6Q LOSS MUTATED	37	10	15
6Q LOSS WILD-TYPE	157	119	174

Figure S98. Get High-res Image Gene #52: '6q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'6q loss' versus 'RACE'

P value = 0.0504 (Fisher's exact test), Q value = 0.23

Table S99. Gene #52: '6q loss' versus Clinical Feature #7: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	1	8	21	472
6Q LOSS MUTATED	1	1	5	55
6Q LOSS WILD-TYPE	0	7	16	417

Figure S99. Get High-res Image Gene #52: '6q loss' versus Clinical Feature #7: 'RACE'

'8p loss' versus 'Time to Death'

P value = 0.0474 (logrank test), Q value = 0.22

Table S100. Gene #55: '8p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	508	125	0.0 - 211.2 (22.4)
8P LOSS MUTATED	16	6	0.2 - 51.9 (19.9)
8P LOSS WILD-TYPE	492	119	0.0 - 211.2 (22.5)

Figure S100. Get High-res Image Gene #55: '8p loss' versus Clinical Feature #1: 'Time to Death'

'8q loss' versus 'Time to Death'

P value = 0.0439 (logrank test), Q value = 0.21

Table S101. Gene #56: '8q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	508	125	0.0 - 211.2 (22.4)
8Q LOSS MUTATED	11	4	0.2 - 51.9 (19.1)
8Q LOSS WILD-TYPE	497	121	0.0 - 211.2 (22.6)

Figure S101. Get High-res Image Gene #56: '8q loss' versus Clinical Feature #1: 'Time to Death'

'9p loss' versus 'Time to Death'

P value = 1.11e-06 (logrank test), Q value = 4.5e-05

Table S102. Gene #57: '9p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	508	125	0.0 - 211.2 (22.4)
9P LOSS MUTATED	116	46	0.1 - 169.8 (21.2)
9P LOSS WILD-TYPE	392	79	0.0 - 211.2 (22.5)

Figure S102. Get High-res Image Gene #57: '9p loss' versus Clinical Feature #1: 'Time to Death'

'9p loss' versus 'YEARS_TO_BIRTH'

P value = 0.00204 (Wilcoxon-test), Q value = 0.024

Table S103. Gene #57: '9p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	511	43.0 (13.3)
9P LOSS MUTATED	116	46.2 (13.2)
9P LOSS WILD-TYPE	395	42.0 (13.3)

Figure S103. Get High-res Image Gene #57: '9p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'9p loss' versus 'RADIATION_THERAPY'

P value = 0.000609 (Fisher's exact test), Q value = 0.0092

Table S104. Gene #57: '9p loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	184	295
9P LOSS MUTATED	25	79
9P LOSS WILD-TYPE	159	216

Figure S104. Get High-res Image Gene #57: '9p loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

'9p loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

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

Table S105. Gene #57: '9p loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	306	86.7 (12.6)
9P LOSS MUTATED	75	83.1 (13.0)
9P LOSS WILD-TYPE	231	87.8 (12.3)

Figure S105. Get High-res Image Gene #57: '9p loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'9p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0589 (Fisher's exact test), Q value = 0.25

Table S106. Gene #57: '9p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	194	129	189
9P LOSS MUTATED	55	23	39
9P LOSS WILD-TYPE	139	106	150

Figure S106. Get High-res Image Gene #57: '9p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'9q loss' versus 'Time to Death'

P value = 0.0035 (logrank test), Q value = 0.037

Table S107. Gene #58: '9q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	508	125	0.0 - 211.2 (22.4)
9Q LOSS MUTATED	50	21	0.1 - 169.8 (21.6)
9Q LOSS WILD-TYPE	458	104	0.0 - 211.2 (22.5)

Figure S107. Get High-res Image Gene #58: '9q loss' versus Clinical Feature #1: 'Time to Death'

'9q loss' versus 'YEARS_TO_BIRTH'

P value = 0.00595 (Wilcoxon-test), Q value = 0.055

Table S108. Gene #58: '9q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	511	43.0 (13.3)
9Q LOSS MUTATED	50	48.1 (14.7)
9Q LOSS WILD-TYPE	461	42.4 (13.1)

Figure S108. Get High-res Image Gene #58: '9q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'9q loss' versus 'RADIATION_THERAPY'

P value = 0.011 (Fisher's exact test), Q value = 0.084

Table S109. Gene #58: '9q loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	184	295
9Q LOSS MUTATED	8	33
9Q LOSS WILD-TYPE	176	262

Figure S109. Get High-res Image Gene #58: '9q loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

'9q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.000364 (Wilcoxon-test), Q value = 0.0059

Table S110. Gene #58: '9q loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	306	86.7 (12.6)
9Q LOSS MUTATED	32	80.0 (12.2)
9Q LOSS WILD-TYPE	274	87.4 (12.4)

Figure S110. Get High-res Image Gene #58: '9q loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'10p loss' versus 'Time to Death'

P value = 0 (logrank test), Q value = 0

Table S111. Gene #59: '10p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	508	125	0.0 - 211.2 (22.4)
10P LOSS MUTATED	83	49	0.1 - 134.3 (16.2)
10P LOSS WILD-TYPE	425	76	0.0 - 211.2 (25.6)

Figure S111. Get High-res Image Gene #59: '10p loss' versus Clinical Feature #1: 'Time to Death'

'10p loss' versus 'YEARS_TO_BIRTH'

P value = 5.96e-20 (Wilcoxon-test), Q value = 1.3e-17

Table S112. Gene #59: '10p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	511	43.0 (13.3)
10P LOSS MUTATED	83	55.6 (11.0)
10P LOSS WILD-TYPE	428	40.5 (12.4)

Figure S112. Get High-res Image Gene #59: '10p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'10p loss' versus 'RADIATION_THERAPY'

P value = 9.18e-05 (Fisher's exact test), Q value = 0.0021

Table S113. Gene #59: '10p loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	184	295
10P LOSS MUTATED	14	61
10P LOSS WILD-TYPE	170	234

Figure S113. Get High-res Image Gene #59: '10p loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

'10p loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.000203 (Wilcoxon-test), Q value = 0.0039

Table S114. Gene #59: '10p loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	306	86.7 (12.6)
10P LOSS MUTATED	52	80.4 (14.9)
10P LOSS WILD-TYPE	254	88.0 (11.7)

Figure S114. Get High-res Image Gene #59: '10p loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'10p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00011 (Fisher's exact test), Q value = 0.0022

Table S115. Gene #59: '10p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	194	129	189
10P LOSS MUTATED	49	16	18
10P LOSS WILD-TYPE	145	113	171

Figure S115. Get High-res Image Gene #59: '10p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'10p loss' versus 'RACE'

P value = 0.00867 (Fisher's exact test), Q value = 0.072

Table S116. Gene #59: '10p loss' versus Clinical Feature #7: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	1	8	21	472
10P LOSS MUTATED	1	1	8	72
10P LOSS WILD-TYPE	0	7	13	400

Figure S116. Get High-res Image Gene #59: '10p loss' versus Clinical Feature #7: 'RACE'

'10q loss' versus 'Time to Death'

P value = 0 (logrank test), Q value = 0

Table S117. Gene #60: '10q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	508	125	0.0 - 211.2 (22.4)
10Q LOSS MUTATED	97	55	0.1 - 172.8 (17.6)
10Q LOSS WILD-TYPE	411	70	0.0 - 211.2 (25.5)

Figure S117. Get High-res Image Gene #60: '10q loss' versus Clinical Feature #1: 'Time to Death'

'10q loss' versus 'YEARS_TO_BIRTH'

P value = 2.9e-17 (Wilcoxon-test), Q value = 4.7e-15

Table S118. Gene #60: '10q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	511	43.0 (13.3)
10Q LOSS MUTATED	97	53.4 (12.3)
10Q LOSS WILD-TYPE	414	40.5 (12.4)

Figure S118. Get High-res Image Gene #60: '10q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'10q loss' versus 'RADIATION_THERAPY'

P value = 2.96e-06 (Fisher's exact test), Q value = 0.00011

Table S119. Gene #60: '10q loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	184	295
10Q LOSS MUTATED	15	73
10Q LOSS WILD-TYPE	169	222

Figure S119. Get High-res Image Gene #60: '10q loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

'10q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.000212 (Wilcoxon-test), Q value = 0.0039

Table S120. Gene #60: '10q loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	306	86.7 (12.6)
10Q LOSS MUTATED	60	80.8 (14.9)
10Q LOSS WILD-TYPE	246	88.1 (11.6)

Figure S120. Get High-res Image Gene #60: '10q loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'10q loss' versus 'HISTOLOGICAL_TYPE'

P value = 3e-05 (Fisher's exact test), Q value = 0.00078

Table S121. Gene #60: '10q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	194	129	189
10Q LOSS MUTATED	57	19	21
10Q LOSS WILD-TYPE	137	110	168

Figure S121. Get High-res Image Gene #60: '10q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'10q loss' versus 'RACE'

P value = 0.0278 (Fisher's exact test), Q value = 0.16

Table S122. Gene #60: '10q loss' versus Clinical Feature #7: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	1	8	21	472
10Q LOSS MUTATED	1	1	8	86
10Q LOSS WILD-TYPE	0	7	13	386

Figure S122. Get High-res Image Gene #60: '10q loss' versus Clinical Feature #7: 'RACE'

'11p loss' versus 'Time to Death'

P value = 0.0307 (logrank test), Q value = 0.17

Table S123. Gene #61: '11p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	508	125	0.0 - 211.2 (22.4)
11P LOSS MUTATED	63	24	0.2 - 156.2 (20.5)
11P LOSS WILD-TYPE	445	101	0.0 - 211.2 (22.5)

Figure S123. Get High-res Image Gene #61: '11p loss' versus Clinical Feature #1: 'Time to Death'

'11p loss' versus 'RADIATION_THERAPY'

P value = 0.00629 (Fisher's exact test), Q value = 0.057

Table S124. Gene #61: '11p loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	184	295
11P LOSS MUTATED	13	46
11P LOSS WILD-TYPE	171	249

Figure S124. Get High-res Image Gene #61: '11p loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

'11p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00063 (Fisher's exact test), Q value = 0.0093

Table S125. Gene #61: '11p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	194	129	189
11P LOSS MUTATED	37	14	12
11P LOSS WILD-TYPE	157	115	177

Figure S125. Get High-res Image Gene #61: '11p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'11q loss' versus 'Time to Death'

P value = 9.86e-05 (logrank test), Q value = 0.0021

Table S126. Gene #62: '11q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	508	125	0.0 - 211.2 (22.4)
11Q LOSS MUTATED	21	9	0.2 - 54.8 (18.7)
11Q LOSS WILD-TYPE	487	116	0.0 - 211.2 (23.2)

Figure S126. Get High-res Image Gene #62: '11q loss' versus Clinical Feature #1: 'Time to Death'

'11q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0141 (Fisher's exact test), Q value = 0.1

Table S127. Gene #62: '11q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	194	129	189
11Q LOSS MUTATED	13	6	2
11Q LOSS WILD-TYPE	181	123	187

Figure S127. Get High-res Image Gene #62: '11q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'12q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00291 (Fisher's exact test), Q value = 0.032

Table S128. Gene #64: '12q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	194	129	189
12Q LOSS MUTATED	29	14	9
12Q LOSS WILD-TYPE	165	115	180

Figure S128. Get High-res Image Gene #64: '12q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'13q loss' versus 'RADIATION_THERAPY'

P value = 0.000328 (Fisher's exact test), Q value = 0.0054

Table S129. Gene #65: '13q loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	184	295
13Q LOSS MUTATED	26	83
13Q LOSS WILD-TYPE	158	212

Figure S129. Get High-res Image Gene #65: '13q loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

'14q loss' versus 'Time to Death'

P value = 2.47e-05 (logrank test), Q value = 0.00067

Table S130. Gene #66: '14q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	508	125	0.0 - 211.2 (22.4)
14Q LOSS MUTATED	80	33	0.1 - 130.8 (21.3)
14Q LOSS WILD-TYPE	428	92	0.0 - 211.2 (22.9)

Figure S130. Get High-res Image Gene #66: '14q loss' versus Clinical Feature #1: 'Time to Death'

'14q loss' versus 'YEARS_TO_BIRTH'

P value = 3.84e-05 (Wilcoxon-test), Q value = 0.00096

Table S131. Gene #66: '14q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	511	43.0 (13.3)
14Q LOSS MUTATED	81	48.7 (13.2)
14Q LOSS WILD-TYPE	430	41.9 (13.1)

Figure S131. Get High-res Image Gene #66: '14q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'14q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.035 (Wilcoxon-test), Q value = 0.18

Table S132. Gene #66: '14q loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	306	86.7 (12.6)
14Q LOSS MUTATED	51	83.5 (13.1)
14Q LOSS WILD-TYPE	255	87.3 (12.4)

Figure S132. Get High-res Image Gene #66: '14q loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'16p loss' versus 'Time to Death'

P value = 0.052 (logrank test), Q value = 0.23

Table S133. Gene #68: '16p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	508	125	0.0 - 211.2 (22.4)
16P LOSS MUTATED	14	7	2.4 - 78.3 (28.6)
16P LOSS WILD-TYPE	494	118	0.0 - 211.2 (22.2)

Figure S133. Get High-res Image Gene #68: '16p loss' versus Clinical Feature #1: 'Time to Death'

'16p loss' versus 'YEARS_TO_BIRTH'

P value = 0.000244 (Wilcoxon-test), Q value = 0.0043

Table S134. Gene #68: '16p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	511	43.0 (13.3)
16P LOSS MUTATED	14	56.1 (10.7)
16P LOSS WILD-TYPE	497	42.6 (13.2)

Figure S134. Get High-res Image Gene #68: '16p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'16q loss' versus 'YEARS_TO_BIRTH'

P value = 0.000217 (Wilcoxon-test), Q value = 0.0039

Table S135. Gene #69: '16q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	511	43.0 (13.3)
16Q LOSS MUTATED	22	54.3 (13.8)
16Q LOSS WILD-TYPE	489	42.5 (13.1)

Figure S135. Get High-res Image Gene #69: '16q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'16q loss' versus 'RADIATION_THERAPY'

P value = 0.0212 (Fisher's exact test), Q value = 0.13

Table S136. Gene #69: '16q loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	184	295
16Q LOSS MUTATED	3	18
16Q LOSS WILD-TYPE	181	277

Figure S136. Get High-res Image Gene #69: '16q loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

'17p loss' versus 'Time to Death'

P value = 0.0587 (logrank test), Q value = 0.25

Table S137. Gene #70: '17p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	508	125	0.0 - 211.2 (22.4)
17P LOSS MUTATED	14	3	0.1 - 33.3 (15.0)
17P LOSS WILD-TYPE	494	122	0.0 - 211.2 (23.2)

Figure S137. Get High-res Image Gene #70: '17p loss' versus Clinical Feature #1: 'Time to Death'

'17p loss' versus 'YEARS_TO_BIRTH'

P value = 0.0397 (Wilcoxon-test), Q value = 0.2

Table S138. Gene #70: '17p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	511	43.0 (13.3)
17P LOSS MUTATED	14	49.9 (12.3)
17P LOSS WILD-TYPE	497	42.8 (13.3)

Figure S138. Get High-res Image Gene #70: '17p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'17p loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0168 (Wilcoxon-test), Q value = 0.11

Table S139. Gene #70: '17p loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	306	86.7 (12.6)
17P LOSS MUTATED	7	77.1 (9.5)
17P LOSS WILD-TYPE	299	86.9 (12.6)

Figure S139. Get High-res Image Gene #70: '17p loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'17p loss' versus 'ETHNICITY'

P value = 0.0599 (Fisher's exact test), Q value = 0.25

Table S140. Gene #70: '17p loss' versus Clinical Feature #8: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	32	446
17P LOSS MUTATED	3	11
17P LOSS WILD-TYPE	29	435

Figure S140. Get High-res Image Gene #70: '17p loss' versus Clinical Feature #8: 'ETHNICITY'

'18p loss' versus 'YEARS_TO_BIRTH'

P value = 0.00237 (Wilcoxon-test), Q value = 0.027

Table S141. Gene #72: '18p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	511	43.0 (13.3)
18P LOSS MUTATED	67	48.1 (14.6)
18P LOSS WILD-TYPE	444	42.2 (13.0)

Figure S141. Get High-res Image Gene #72: '18p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'18q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0236 (Wilcoxon-test), Q value = 0.14

Table S142. Gene #73: '18q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	511	43.0 (13.3)
18Q LOSS MUTATED	62	47.1 (14.7)
18Q LOSS WILD-TYPE	449	42.4 (13.1)

Figure S142. Get High-res Image Gene #73: '18q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'18q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0326 (Fisher's exact test), Q value = 0.17

Table S143. Gene #73: '18q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	194	129	189
18Q LOSS MUTATED	20	10	32
18Q LOSS WILD-TYPE	174	119	157

Figure S143. Get High-res Image Gene #73: '18q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'19p loss' versus 'RACE'

P value = 0.0219 (Fisher's exact test), Q value = 0.13

Table S144. Gene #74: '19p loss' versus Clinical Feature #7: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	1	8	21	472
19P LOSS MUTATED	0	1	4	20
19P LOSS WILD-TYPE	1	7	17	452

Figure S144. Get High-res Image Gene #74: '19p loss' versus Clinical Feature #7: 'RACE'

'19p loss' versus 'ETHNICITY'

P value = 0.0594 (Fisher's exact test), Q value = 0.25

Table S145. Gene #74: '19p loss' versus Clinical Feature #8: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	32	446
19P LOSS MUTATED	4	19
19P LOSS WILD-TYPE	28	427

Figure S145. Get High-res Image Gene #74: '19p loss' versus Clinical Feature #8: 'ETHNICITY'

'19q loss' versus 'Time to Death'

P value = 0.0024 (logrank test), Q value = 0.027

Table S146. Gene #75: '19q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	508	125	0.0 - 211.2 (22.4)
19Q LOSS MUTATED	206	38	0.1 - 182.3 (24.7)
19Q LOSS WILD-TYPE	302	87	0.0 - 211.2 (20.8)

Figure S146. Get High-res Image Gene #75: '19q loss' versus Clinical Feature #1: 'Time to Death'

'19q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0437 (Wilcoxon-test), Q value = 0.21

Table S147. Gene #75: '19q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	511	43.0 (13.3)
19Q LOSS MUTATED	208	44.2 (12.5)
19Q LOSS WILD-TYPE	303	42.2 (13.8)

Figure S147. Get High-res Image Gene #75: '19q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'19q loss' versus 'RADIATION_THERAPY'

P value = 4.3e-06 (Fisher's exact test), Q value = 0.00015

Table S148. Gene #75: '19q loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	184	295
19Q LOSS MUTATED	100	97
19Q LOSS WILD-TYPE	84	198

Figure S148. Get High-res Image Gene #75: '19q loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

'19q loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00028

Table S149. Gene #75: '19q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	194	129	189
19Q LOSS MUTATED	23	44	142
19Q LOSS WILD-TYPE	171	85	47

Figure S149. Get High-res Image Gene #75: '19q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'20p loss' versus 'RADIATION_THERAPY'

P value = 0.0472 (Fisher's exact test), Q value = 0.22

Table S150. Gene #76: '20p loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	184	295
20P LOSS MUTATED	0	7
20P LOSS WILD-TYPE	184	288

Figure S150. Get High-res Image Gene #76: '20p loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

'21q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00752 (Wilcoxon-test), Q value = 0.066

Table S151. Gene #78: '21q loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	306	86.7 (12.6)
21Q LOSS MUTATED	28	80.7 (13.9)
21Q LOSS WILD-TYPE	278	87.3 (12.3)

Figure S151. Get High-res Image Gene #78: '21q loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'21q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00412 (Fisher's exact test), Q value = 0.042

Table S152. Gene #78: '21q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	194	129	189
21Q LOSS MUTATED	24	7	7
21Q LOSS WILD-TYPE	170	122	182

Figure S152. Get High-res Image Gene #78: '21q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'22q loss' versus 'Time to Death'

P value = 1.94e-08 (logrank test), Q value = 1.2e-06

Table S153. Gene #79: '22q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	508	125	0.0 - 211.2 (22.4)
22Q LOSS MUTATED	57	28	0.1 - 156.2 (19.5)
22Q LOSS WILD-TYPE	451	97	0.0 - 211.2 (23.2)

Figure S153. Get High-res Image Gene #79: '22q loss' versus Clinical Feature #1: 'Time to Death'

'22q loss' versus 'YEARS_TO_BIRTH'

P value = 2.06e-06 (Wilcoxon-test), Q value = 7.8e-05

Table S154. Gene #79: '22q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	511	43.0 (13.3)
22Q LOSS MUTATED	57	51.5 (13.8)
22Q LOSS WILD-TYPE	454	41.9 (12.9)

Figure S154. Get High-res Image Gene #79: '22q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'22q loss' versus 'RADIATION_THERAPY'

P value = 0.0483 (Fisher's exact test), Q value = 0.22

Table S155. Gene #79: '22q loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	184	295
22Q LOSS MUTATED	13	38
22Q LOSS WILD-TYPE	171	257

Figure S155. Get High-res Image Gene #79: '22q loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

'22q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00505 (Wilcoxon-test), Q value = 0.05

Table S156. Gene #79: '22q loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	306	86.7 (12.6)
22Q LOSS MUTATED	35	80.6 (15.1)
22Q LOSS WILD-TYPE	271	87.5 (12.0)

Figure S156. Get High-res Image Gene #79: '22q loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'xq loss' versus 'Time to Death'

P value = 0.00654 (logrank test), Q value = 0.059

Table S157. Gene #81: 'xq loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	508	125	0.0 - 211.2 (22.4)
XQ LOSS MUTATED	69	23	0.1 - 134.3 (18.6)
XQ LOSS WILD-TYPE	439	102	0.0 - 211.2 (23.6)

Figure S157. Get High-res Image Gene #81: 'xq loss' versus Clinical Feature #1: 'Time to Death'

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/LGG-TP/22533657/transformed.cor.cli.txt
Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/LGG-TP/22506744/LGG-TP.merged_data.txt
Number of patients = 512
Number of significantly arm-level cnvs = 81
Number of selected clinical features = 8
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.

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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