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, 155 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'.
4p gain cnv correlated to 'HISTOLOGICAL_TYPE'.
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'.
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', '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, 155 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	151 (29%)	361	1.69e-07 (7.31e-06)	3.28e-10 (2.65e-08)	0.495 (0.821)	0.000867 (0.012)	0.00641 (0.0526)	0.0391 (0.195)	0.00963 (0.0717)	0.556 (0.859)
6q loss	62 (12%)	450	1.96e-05 (0.000489)	0.0291 (0.161)	0.414 (0.747)	0.0256 (0.147)	0.000617 (0.00952)	0.00136 (0.0173)	0.0512 (0.225)	0.563 (0.863)
10p loss	83 (16%)	429	0 (0)	5.96e-20 (1.29e-17)	0.81 (0.984)	0.000138 (0.00271)	0.000218 (0.00392)	9e-05 (0.00189)	0.00884 (0.0666)	0.804 (0.983)
10q loss	96 (19%)	416	0 (0)	2.03e-17 (3.29e-15)	0.649 (0.905)	4.74e-06 (0.000154)	0.000462 (0.00749)	4e-05 (0.00096)	0.0252 (0.147)	0.484 (0.82)
7p gain	121 (24%)	391	6.05e-09 (4.35e-07)	2.93e-10 (2.65e-08)	0.21 (0.514)	0.000824 (0.0116)	0.00106 (0.0138)	0.204 (0.506)	0.0167 (0.109)	1 (1.00)
9p loss	117 (23%)	395	3.1e-06 (0.000112)	0.00204 (0.0232)	1 (1.00)	0.000963 (0.013)	0.0022 (0.0246)	0.0582 (0.246)	0.607 (0.894)	0.669 (0.905)
1p gain	13 (3%)	499	0.00396 (0.0401)	0.0126 (0.0884)	0.263 (0.575)	0.0341 (0.179)	0.811 (0.984)	0.0083 (0.0648)	0.555 (0.859)	1 (1.00)
20p gain	43 (8%)	469	8.27e-12 (8.93e-10)	2.19e-08 (1.42e-06)	0.873 (1.00)	0.0401 (0.199)	0.0124 (0.0882)	0.199 (0.499)	0.388 (0.721)	0.503 (0.826)
20q gain	43 (8%)	469	1.17e-12 (1.52e-10)	2.98e-08 (1.75e-06)	0.423 (0.757)	0.0405 (0.199)	0.0124 (0.0882)	0.304 (0.626)	0.626 (0.899)	0.503 (0.826)
xq gain	39 (8%)	473	0.32 (0.636)	0.0496 (0.225)	0.0043 (0.0416)	0.294 (0.616)	0.515 (0.832)	0.00743 (0.0587)	0.593 (0.884)	0.0194 (0.123)
1p loss	184 (36%)	328	9.05e-05 (0.00189)	0.00101 (0.0134)	0.853 (1.00)	5.62e-08 (3.03e-06)	0.269 (0.58)	1e-05 (0.00027)	0.317 (0.636)	0.704 (0.922)
9q loss	50 (10%)	462	0.00858 (0.0654)	0.00595 (0.0516)	1 (1.00)	0.011 (0.0803)	0.000384 (0.00638)	0.879 (1.00)	0.135 (0.401)	1 (1.00)
19q loss	209 (41%)	303	0.00139 (0.0173)	0.0437 (0.21)	0.928 (1.00)	4.1e-06 (0.00014)	0.322 (0.637)	1e-05 (0.00027)	0.917 (1.00)	0.0929 (0.322)
22q loss	57 (11%)	455	8.53e-08 (4.25e-06)	2.06e-06 (8.32e-05)	0.482 (0.82)	0.035 (0.179)	0.00527 (0.0481)	0.12 (0.367)	0.175 (0.453)	0.56 (0.863)
9q gain	24 (5%)	488	0.175 (0.453)	0.0775 (0.292)	0.00268 (0.0294)	0.00173 (0.0212)	0.567 (0.865)	0.0586 (0.246)	0.213 (0.516)	0.661 (0.905)
10p gain	57 (11%)	455	0.677 (0.905)	0.0215 (0.134)	0.258 (0.574)	0.011 (0.0803)	0.207 (0.509)	0.00017 (0.00324)	1 (1.00)	0.136 (0.402)
15q gain	11 (2%)	501	0.0508 (0.225)	0.0259 (0.147)	1 (1.00)	0.542 (0.851)	0.0138 (0.0929)	0.404 (0.74)	0.495 (0.821)	1 (1.00)
17p gain	20 (4%)	492	0.00555 (0.0499)	0.0176 (0.114)	0.106 (0.346)	0.489 (0.821)	0.666 (0.905)	0.0595 (0.249)	0.221 (0.532)	1 (1.00)
19p gain	100 (20%)	412	0.702 (0.921)	0.013 (0.0906)	0.22 (0.532)	0.0581 (0.246)	0.483 (0.82)	1e-05 (0.00027)	0.532 (0.843)	0.111 (0.356)
4p loss	71 (14%)	441	0.642 (0.905)	0.00404 (0.0403)	0.0542 (0.236)	1 (1.00)	0.958 (1.00)	0.0003 (0.00512)	0.511 (0.832)	0.796 (0.982)
6p loss	30 (6%)	482	8.3e-05 (0.00185)	0.0548 (0.237)	0.573 (0.865)	0.0578 (0.246)	0.0764 (0.29)	0.231 (0.546)	0.0626 (0.258)	1 (1.00)
11p loss	63 (12%)	449	0.0222 (0.137)	0.265 (0.575)	0.343 (0.662)	0.00625 (0.0526)	0.177 (0.454)	0.00065 (0.0098)	0.561 (0.863)	0.784 (0.975)
14q loss	80 (16%)	432	2.75e-06 (0.000105)	1.66e-05 (0.000431)	0.903 (1.00)	0.156 (0.437)	0.0339 (0.179)	0.258 (0.574)	0.228 (0.543)	0.603 (0.892)
17p loss	13 (3%)	499	0.0351 (0.179)	0.0739 (0.285)	0.263 (0.575)	1 (1.00)	0.00849 (0.0654)	0.726 (0.941)	1 (1.00)	0.0493 (0.225)
3p gain	11 (2%)	501	0.0362 (0.183)	0.0849 (0.307)	0.551 (0.856)	1 (1.00)	0.813 (0.985)	0.0287 (0.16)	1 (1.00)	1 (1.00)
3q gain	8 (2%)	504	0.00194 (0.0231)	0.0332 (0.179)	0.476 (0.816)	0.413 (0.747)	0.304 (0.626)	0.0914 (0.32)	1 (1.00)	1 (1.00)
5p gain	11 (2%)	501	0.0283 (0.16)	0.0321 (0.176)	1 (1.00)	0.542 (0.851)	0.8 (0.982)	0.245 (0.561)	0.0809 (0.297)	1 (1.00)
5q gain	8 (2%)	504	0.0505 (0.225)	0.0748 (0.286)	1 (1.00)	1 (1.00)	0.542 (0.851)	0.9 (1.00)	0.0439 (0.21)	1 (1.00)
9p gain	17 (3%)	495	0.285 (0.6)	0.104 (0.344)	0.0442 (0.21)	0.0351 (0.179)	0.583 (0.873)	0.236 (0.55)	0.655 (0.905)	1 (1.00)
11p gain	31 (6%)	481	0.223 (0.536)	0.0384 (0.193)	0.266 (0.575)	0.244 (0.561)	0.436 (0.768)	0.00674 (0.0546)	1 (1.00)	0.442 (0.774)
19q gain	25 (5%)	487	1.32e-07 (6.12e-06)	7.02e-06 (0.000217)	0.416 (0.747)	0.0683 (0.279)	0.0686 (0.279)	0.156 (0.437)	0.0964 (0.325)	0.67 (0.905)
22q gain	23 (4%)	489	0.768 (0.974)	0.0457 (0.214)	0.831 (0.999)	0.122 (0.371)	0.194 (0.487)	0.00411 (0.0404)	0.732 (0.947)	0.159 (0.442)
3p loss	30 (6%)	482	0.0466 (0.217)	0.883 (1.00)	0.45 (0.785)	0.242 (0.56)	0.00198 (0.0231)	0.914 (1.00)	0.313 (0.633)	0.431 (0.766)
5p loss	34 (7%)	478	0.67 (0.905)	0.342 (0.662)	0.724 (0.94)	0.00728 (0.0583)	0.366 (0.701)	0.0139 (0.0929)	0.675 (0.905)	0.154 (0.436)
5q loss	33 (6%)	479	0.165 (0.445)	0.255 (0.571)	0.47 (0.812)	0.00311 (0.0335)	0.921 (1.00)	0.0247 (0.146)	0.669 (0.905)	0.713 (0.93)
11q loss	21 (4%)	491	9.85e-05 (0.00199)	0.149 (0.427)	1 (1.00)	0.081 (0.297)	0.0841 (0.306)	0.0131 (0.0906)	1 (1.00)	1 (1.00)
16p loss	14 (3%)	498	0.0509 (0.225)	0.000244 (0.00427)	1 (1.00)	0.266 (0.575)	0.151 (0.429)	0.744 (0.96)	0.582 (0.873)	0.239 (0.556)
16q loss	22 (4%)	490	0.0737 (0.285)	0.000217 (0.00392)	0.664 (0.905)	0.021 (0.132)	0.075 (0.286)	0.512 (0.832)	0.493 (0.821)	0.652 (0.905)
18q loss	62 (12%)	450	0.669 (0.905)	0.0236 (0.141)	0.499 (0.824)	0.885 (1.00)	0.878 (1.00)	0.0326 (0.178)	0.105 (0.345)	0.784 (0.975)
19p loss	25 (5%)	487	0.824 (0.993)	0.804 (0.983)	1 (1.00)	0.513 (0.832)	0.0779 (0.292)	0.933 (1.00)	0.0187 (0.12)	0.0514 (0.225)
21q loss	36 (7%)	476	0.906 (1.00)	0.617 (0.897)	0.493 (0.821)	0.26 (0.574)	0.00633 (0.0526)	0.00359 (0.0369)	0.57 (0.865)	1 (1.00)
1q gain	23 (4%)	489	0.364 (0.699)	5.1e-05 (0.00118)	0.522 (0.836)	0.655 (0.905)	0.115 (0.362)	0.0807 (0.297)	0.278 (0.594)	0.385 (0.721)
4p gain	13 (3%)	499	0.722 (0.939)	0.646 (0.905)	1 (1.00)	0.387 (0.721)	0.797 (0.982)	0.0235 (0.141)	0.188 (0.477)	1 (1.00)
8q gain	56 (11%)	456	0.545 (0.852)	0.166 (0.445)	0.67 (0.905)	0.0256 (0.147)	0.278 (0.594)	0.128 (0.381)	0.641 (0.905)	0.143 (0.418)
10q gain	12 (2%)	500	0.926 (1.00)	0.251 (0.567)	1 (1.00)	0.385 (0.721)	0.757 (0.969)	0.00351 (0.0367)	0.107 (0.347)	0.164 (0.444)
12p gain	33 (6%)	479	0.327 (0.642)	0.438 (0.769)	0.208 (0.509)	0.0227 (0.139)	0.854 (1.00)	0.33 (0.645)	0.434 (0.767)	1 (1.00)
12q gain	16 (3%)	496	0.00579 (0.0514)	0.307 (0.627)	0.317 (0.636)	0.425 (0.757)	0.0739 (0.285)	0.859 (1.00)	0.172 (0.453)	0.615 (0.896)
13q gain	6 (1%)	506	0.411 (0.747)	0.94 (1.00)	1 (1.00)	0.0339 (0.179)	0.0688 (0.279)	1 (1.00)	1 (1.00)	1 (1.00)
16q gain	19 (4%)	493	0.416 (0.747)	0.606 (0.894)	0.49 (0.821)	0.461 (0.798)	0.629 (0.902)	0.0142 (0.0942)	0.677 (0.905)	0.623 (0.897)
17q gain	23 (4%)	489	0.00316 (0.0335)	0.118 (0.367)	0.0858 (0.309)	0.664 (0.905)	0.946 (1.00)	0.276 (0.592)	0.261 (0.574)	0.636 (0.905)
18p gain	17 (3%)	495	0.000687 (0.0101)	0.993 (1.00)	0.621 (0.897)	0.613 (0.896)	0.39 (0.722)	0.383 (0.721)	0.283 (0.599)	0.615 (0.896)
18q gain	13 (3%)	499	0.000516 (0.00815)	0.781 (0.975)	1 (1.00)	0.0915 (0.32)	0.514 (0.832)	0.458 (0.796)	0.192 (0.484)	1 (1.00)
21q gain	24 (5%)	488	0.178 (0.455)	0.00597 (0.0516)	0.401 (0.737)	0.177 (0.454)	0.124 (0.372)	0.868 (1.00)	0.408 (0.745)	0.393 (0.726)
xp gain	21 (4%)	491	0.818 (0.987)	0.994 (1.00)	0.119 (0.367)	0.246 (0.561)	0.5 (0.824)	0.0349 (0.179)	0.259 (0.574)	1 (1.00)
1q loss	25 (5%)	487	0.524 (0.836)	0.0945 (0.322)	0.837 (1.00)	1 (1.00)	0.596 (0.886)	0.0045 (0.0423)	0.211 (0.514)	1 (1.00)
2p loss	21 (4%)	491	0.302 (0.625)	0.528 (0.839)	0.656 (0.905)	0.0138 (0.0929)	0.0695 (0.28)	0.229 (0.543)	1 (1.00)	0.385 (0.721)
2q loss	18 (4%)	494	0.904 (1.00)	0.48 (0.82)	0.81 (0.984)	0.12 (0.367)	0.228 (0.543)	0.0492 (0.225)	1 (1.00)	0.623 (0.897)
3q loss	28 (5%)	484	0.0245 (0.146)	0.443 (0.775)	0.697 (0.918)	0.3 (0.623)	0.0982 (0.328)	0.969 (1.00)	0.28 (0.594)	0.7 (0.92)
4q loss	92 (18%)	420	0.32 (0.636)	0.15 (0.429)	0.203 (0.503)	0.712 (0.93)	0.745 (0.96)	0.00617 (0.0526)	0.871 (1.00)	1 (1.00)
8p loss	17 (3%)	495	0.045 (0.213)	0.174 (0.453)	0.81 (0.984)	0.0912 (0.32)	0.334 (0.649)	0.387 (0.721)	0.113 (0.358)	0.317 (0.636)
8q loss	11 (2%)	501	0.0438 (0.21)	0.111 (0.356)	0.551 (0.856)	0.163 (0.444)	0.514 (0.832)	0.8 (0.982)	0.0931 (0.322)	0.164 (0.444)
12q loss	51 (10%)	461	0.862 (1.00)	0.161 (0.444)	0.658 (0.905)	0.163 (0.444)	0.944 (1.00)	0.00457 (0.0423)	0.788 (0.975)	0.234 (0.55)
13q loss	116 (23%)	396	0.382 (0.721)	0.68 (0.905)	0.168 (0.449)	0.000824 (0.0116)	0.146 (0.426)	0.568 (0.865)	0.298 (0.622)	0.388 (0.721)
18p loss	68 (13%)	444	0.672 (0.905)	0.002 (0.0231)	0.116 (0.363)	1 (1.00)	0.474 (0.815)	0.147 (0.426)	0.1 (0.333)	0.784 (0.975)
20p loss	7 (1%)	505	0.9 (1.00)	0.858 (1.00)	0.251 (0.567)	0.0469 (0.217)	0.434 (0.767)	0.494 (0.821)	0.148 (0.426)	0.386 (0.721)
xq loss	71 (14%)	441	0.00453 (0.0423)	0.174 (0.453)	0.523 (0.836)	0.0954 (0.324)	0.164 (0.444)	0.76 (0.969)	0.653 (0.905)	1 (1.00)
2p gain	14 (3%)	498	0.148 (0.426)	0.0783 (0.292)	0.787 (0.975)	0.387 (0.721)	0.492 (0.821)	0.549 (0.856)	1 (1.00)	0.599 (0.888)
2q gain	13 (3%)	499	0.319 (0.636)	0.172 (0.453)	0.577 (0.868)	0.141 (0.415)	0.492 (0.821)	0.562 (0.863)	1 (1.00)	0.569 (0.865)
4q gain	6 (1%)	506	0.0617 (0.256)	0.174 (0.453)	0.697 (0.918)	0.413 (0.747)		0.113 (0.358)	1 (1.00)	1 (1.00)
6p gain	7 (1%)	505	0.688 (0.912)	0.123 (0.372)	0.251 (0.567)	0.0865 (0.31)	0.815 (0.986)	0.236 (0.55)	1 (1.00)	1 (1.00)
8p gain	46 (9%)	466	0.614 (0.896)	0.752 (0.967)	0.534 (0.845)	0.0726 (0.285)	0.0981 (0.328)	0.322 (0.637)	1 (1.00)	0.516 (0.832)
11q gain	58 (11%)	454	0.166 (0.445)	0.122 (0.371)	0.263 (0.575)	0.774 (0.975)	0.787 (0.975)	0.235 (0.55)	0.901 (1.00)	0.767 (0.974)
14q gain	4 (1%)	508	0.11 (0.353)	0.252 (0.567)	1 (1.00)	0.642 (0.905)	0.973 (1.00)	0.839 (1.00)	1 (1.00)	0.243 (0.56)
16p gain	17 (3%)	495	0.677 (0.905)	0.0716 (0.283)	0.621 (0.897)	0.306 (0.627)	0.762 (0.971)	0.0933 (0.322)	0.632 (0.904)	0.615 (0.896)
7p loss	3 (1%)	509	0.652 (0.905)	0.643 (0.905)	0.588 (0.878)	0.525 (0.836)		0.787 (0.975)	1 (1.00)	1 (1.00)
7q loss	3 (1%)	509	0.852 (1.00)	0.945 (1.00)	1 (1.00)	0.525 (0.836)	0.973 (1.00)	0.788 (0.975)	1 (1.00)	1 (1.00)
12p loss	26 (5%)	486	0.571 (0.865)	0.172 (0.453)	0.686 (0.911)	0.299 (0.622)	0.312 (0.633)	0.12 (0.367)	1 (1.00)	0.399 (0.734)
15q loss	51 (10%)	461	0.308 (0.628)	0.342 (0.662)	0.658 (0.905)	0.203 (0.503)	0.789 (0.975)	0.647 (0.905)	0.786 (0.975)	0.759 (0.969)
17q loss	8 (2%)	504	0.424 (0.757)	0.158 (0.442)	1 (1.00)	0.68 (0.905)	0.0717 (0.283)	0.754 (0.967)	1 (1.00)	0.0944 (0.322)
20q loss	3 (1%)	509	0.931 (1.00)	0.966 (1.00)	0.0877 (0.312)	1 (1.00)	0.326 (0.642)	0.473 (0.814)	1 (1.00)	0.188 (0.477)
xp loss	99 (19%)	413	0.284 (0.599)	0.78 (0.975)	0.574 (0.865)	0.0715 (0.283)	0.334 (0.649)	0.675 (0.905)	0.691 (0.914)	0.105 (0.345)

'1p gain' versus 'Time to Death'

P value = 0.00396 (logrank test), Q value = 0.04

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

	nPatients	nDeath	Duration Range (Median), Month
ALL	509	121	0.0 - 211.2 (20.8)
1P GAIN MUTATED	13	6	0.2 - 51.9 (19.1)
1P GAIN WILD-TYPE	496	115	0.0 - 211.2 (21.0)

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 = 0.088

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 = 0.0341 (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	293
1P GAIN MUTATED	1	11
1P GAIN WILD-TYPE	183	282

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

'1p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0083 (Fisher's exact test), Q value = 0.065

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 = 0.0362 (logrank test), Q value = 0.18

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

	nPatients	nDeath	Duration Range (Median), Month
ALL	509	121	0.0 - 211.2 (20.8)
3P GAIN MUTATED	11	4	0.2 - 49.9 (17.3)
3P GAIN WILD-TYPE	498	117	0.0 - 211.2 (21.2)

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

'3p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0287 (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 = 0.00194 (logrank test), Q value = 0.023

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

	nPatients	nDeath	Duration Range (Median), Month
ALL	509	121	0.0 - 211.2 (20.8)
3Q GAIN MUTATED	8	4	0.2 - 47.8 (13.1)
3Q GAIN WILD-TYPE	501	117	0.0 - 211.2 (21.0)

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 = 0.18

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'

'4p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0235 (Fisher's exact test), Q value = 0.14

Table S10. Gene #7: '4p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	194	129	189
4P GAIN MUTATED	9	0	4
4P GAIN WILD-TYPE	185	129	185

Figure S10. Get High-res Image Gene #7: '4p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'5p gain' versus 'Time to Death'

P value = 0.0283 (logrank test), Q value = 0.16

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

	nPatients	nDeath	Duration Range (Median), Month
ALL	509	121	0.0 - 211.2 (20.8)
5P GAIN MUTATED	11	6	2.5 - 62.2 (24.4)
5P GAIN WILD-TYPE	498	115	0.0 - 211.2 (20.8)

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 = 0.18

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 = 0.0505 (logrank test), Q value = 0.23

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

	nPatients	nDeath	Duration Range (Median), Month
ALL	509	121	0.0 - 211.2 (20.8)
5Q GAIN MUTATED	8	4	2.5 - 54.8 (19.5)
5Q GAIN WILD-TYPE	501	117	0.0 - 211.2 (20.8)

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

'5q gain' versus 'RACE'

P value = 0.0439 (Fisher's exact test), Q value = 0.21

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	5
5Q GAIN WILD-TYPE	1	7	20	467

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

'7p gain' versus 'Time to Death'

P value = 6.05e-09 (logrank test), Q value = 4.4e-07

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

	nPatients	nDeath	Duration Range (Median), Month
ALL	509	121	0.0 - 211.2 (20.8)
7P GAIN MUTATED	121	49	0.1 - 211.2 (18.4)
7P GAIN WILD-TYPE	388	72	0.0 - 182.3 (23.2)

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 = 2.93e-10 (Wilcoxon-test), Q value = 2.7e-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	121	49.7 (12.8)
7P GAIN WILD-TYPE	390	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 = 0.000824 (Fisher's exact test), Q value = 0.012

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

nPatients	NO	YES
ALL	184	293
7P GAIN MUTATED	28	84
7P GAIN WILD-TYPE	156	209

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

'7p gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00106 (Wilcoxon-test), Q value = 0.014

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

	nPatients	Mean (Std.Dev)
ALL	306	86.6 (12.6)
7P GAIN MUTATED	74	81.9 (15.3)
7P GAIN WILD-TYPE	232	88.1 (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 = 0.0167 (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	108
7P GAIN WILD-TYPE	0	6	11	364

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

'7q gain' versus 'Time to Death'

P value = 1.69e-07 (logrank test), Q value = 7.3e-06

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

	nPatients	nDeath	Duration Range (Median), Month
ALL	509	121	0.0 - 211.2 (20.8)
7Q GAIN MUTATED	151	56	0.1 - 211.2 (18.5)
7Q GAIN WILD-TYPE	358	65	0.0 - 182.3 (23.3)

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 = 3.28e-10 (Wilcoxon-test), Q value = 2.7e-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	151	48.7 (13.1)
7Q GAIN WILD-TYPE	360	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 = 0.000867 (Fisher's exact test), Q value = 0.012

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

nPatients	NO	YES
ALL	184	293
7Q GAIN MUTATED	37	101
7Q GAIN WILD-TYPE	147	192

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

'7q gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00641 (Wilcoxon-test), Q value = 0.053

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

	nPatients	Mean (Std.Dev)
ALL	306	86.6 (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 = 0.0391 (Fisher's exact test), Q value = 0.2

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

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	194	129	189
7Q GAIN MUTATED	68	39	44
7Q GAIN WILD-TYPE	126	90	145

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

'7q gain' versus 'RACE'

P value = 0.00963 (Fisher's exact test), Q value = 0.072

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	135
7Q GAIN WILD-TYPE	0	5	9	337

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

'8q gain' versus 'RADIATION_THERAPY'

P value = 0.0256 (Fisher's exact test), Q value = 0.15

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

nPatients	NO	YES
ALL	184	293
8Q GAIN MUTATED	13	40
8Q GAIN WILD-TYPE	171	253

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 = 0.0351 (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	293
9P GAIN MUTATED	2	14
9P GAIN WILD-TYPE	182	279

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 = 0.029

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 = 0.00173 (Fisher's exact test), Q value = 0.021

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

nPatients	NO	YES
ALL	184	293
9Q GAIN MUTATED	2	21
9Q GAIN WILD-TYPE	182	272

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 = 0.011 (Fisher's exact test), Q value = 0.08

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

nPatients	NO	YES
ALL	184	293
10P GAIN MUTATED	12	42
10P GAIN WILD-TYPE	172	251

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

'10p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00017 (Fisher's exact test), Q value = 0.0032

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 = 0.00351 (Fisher's exact test), Q value = 0.037

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

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	194	129	189
10Q GAIN MUTATED	10	0	2
10Q GAIN WILD-TYPE	184	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 = 0.0384 (Wilcoxon-test), Q value = 0.19

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	31	48.4 (14.8)
11P GAIN WILD-TYPE	480	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 = 0.00674 (Fisher's exact test), Q value = 0.055

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

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	194	129	189
11P GAIN MUTATED	4	10	17
11P GAIN WILD-TYPE	190	119	172

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

'12p gain' versus 'RADIATION_THERAPY'

P value = 0.0227 (Fisher's exact test), Q value = 0.14

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

nPatients	NO	YES
ALL	184	293
12P GAIN MUTATED	6	25
12P GAIN WILD-TYPE	178	268

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

'12q gain' versus 'Time to Death'

P value = 0.00579 (logrank test), Q value = 0.051

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

	nPatients	nDeath	Duration Range (Median), Month
ALL	509	121	0.0 - 211.2 (20.8)
12Q GAIN MUTATED	16	9	1.2 - 84.3 (27.3)
12Q GAIN WILD-TYPE	493	112	0.0 - 211.2 (20.7)

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

'13q gain' versus 'RADIATION_THERAPY'

P value = 0.0339 (Fisher's exact test), Q value = 0.18

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

nPatients	NO	YES
ALL	184	293
13Q GAIN MUTATED	5	1
13Q GAIN WILD-TYPE	179	292

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

'15q gain' versus 'Time to Death'

P value = 0.0508 (logrank test), Q value = 0.23

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

	nPatients	nDeath	Duration Range (Median), Month
ALL	509	121	0.0 - 211.2 (20.8)
15Q GAIN MUTATED	11	6	2.4 - 117.4 (24.3)
15Q GAIN WILD-TYPE	498	115	0.0 - 211.2 (20.8)

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 = 0.0138 (Wilcoxon-test), Q value = 0.093

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

	nPatients	Mean (Std.Dev)
ALL	306	86.6 (12.6)
15Q GAIN MUTATED	10	72.0 (19.9)
15Q GAIN WILD-TYPE	296	87.1 (12.0)

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

'16q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0142 (Fisher's exact test), Q value = 0.094

Table S44. 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 S44. Get High-res Image Gene #28: '16q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'17p gain' versus 'Time to Death'

P value = 0.00555 (logrank test), Q value = 0.05

Table S45. Gene #29: '17p gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	509	121	0.0 - 211.2 (20.8)
17P GAIN MUTATED	20	8	8.1 - 62.2 (20.0)
17P GAIN WILD-TYPE	489	113	0.0 - 211.2 (20.8)

Figure S45. 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 S46. 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 S46. Get High-res Image Gene #29: '17p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'17p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0595 (Fisher's exact test), Q value = 0.25

Table S47. 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 S47. Get High-res Image Gene #29: '17p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'17q gain' versus 'Time to Death'

P value = 0.00316 (logrank test), Q value = 0.034

Table S48. Gene #30: '17q gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	509	121	0.0 - 211.2 (20.8)
17Q GAIN MUTATED	23	9	5.8 - 62.2 (19.0)
17Q GAIN WILD-TYPE	486	112	0.0 - 211.2 (20.9)

Figure S48. Get High-res Image Gene #30: '17q gain' versus Clinical Feature #1: 'Time to Death'

'18p gain' versus 'Time to Death'

P value = 0.000687 (logrank test), Q value = 0.01

Table S49. Gene #31: '18p gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	509	121	0.0 - 211.2 (20.8)
18P GAIN MUTATED	17	9	0.2 - 51.9 (20.8)
18P GAIN WILD-TYPE	492	112	0.0 - 211.2 (20.9)

Figure S49. Get High-res Image Gene #31: '18p gain' versus Clinical Feature #1: 'Time to Death'

'18q gain' versus 'Time to Death'

P value = 0.000516 (logrank test), Q value = 0.0081

Table S50. Gene #32: '18q gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	509	121	0.0 - 211.2 (20.8)
18Q GAIN MUTATED	13	8	0.2 - 51.9 (29.1)
18Q GAIN WILD-TYPE	496	113	0.0 - 211.2 (20.8)

Figure S50. Get High-res Image Gene #32: '18q gain' versus Clinical Feature #1: 'Time to Death'

'19p gain' versus 'YEARS_TO_BIRTH'

P value = 0.013 (Wilcoxon-test), Q value = 0.091

Table S51. Gene #33: '19p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	511	43.0 (13.3)
19P GAIN MUTATED	99	46.2 (14.2)
19P GAIN WILD-TYPE	412	42.2 (13.0)

Figure S51. Get High-res Image Gene #33: '19p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'19p gain' versus 'RADIATION_THERAPY'

P value = 0.0581 (Fisher's exact test), Q value = 0.25

Table S52. Gene #33: '19p gain' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	184	293
19P GAIN MUTATED	44	49
19P GAIN WILD-TYPE	140	244

Figure S52. 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 = 0.00027

Table S53. Gene #33: '19p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	194	129	189
19P GAIN MUTATED	20	19	61
19P GAIN WILD-TYPE	174	110	128

Figure S53. Get High-res Image Gene #33: '19p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'19q gain' versus 'Time to Death'

P value = 1.32e-07 (logrank test), Q value = 6.1e-06

Table S54. Gene #34: '19q gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	509	121	0.0 - 211.2 (20.8)
19Q GAIN MUTATED	25	11	0.2 - 54.8 (16.8)
19Q GAIN WILD-TYPE	484	110	0.0 - 211.2 (21.5)

Figure S54. 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 = 0.00022

Table S55. 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 S55. Get High-res Image Gene #34: '19q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'20p gain' versus 'Time to Death'

P value = 8.27e-12 (logrank test), Q value = 8.9e-10

Table S56. Gene #35: '20p gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	509	121	0.0 - 211.2 (20.8)
20P GAIN MUTATED	43	21	0.5 - 54.8 (16.2)
20P GAIN WILD-TYPE	466	100	0.0 - 211.2 (21.6)

Figure S56. Get High-res Image Gene #35: '20p gain' versus Clinical Feature #1: 'Time to Death'

'20p gain' versus 'YEARS_TO_BIRTH'

P value = 2.19e-08 (Wilcoxon-test), Q value = 1.4e-06

Table S57. Gene #35: '20p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	511	43.0 (13.3)
20P GAIN MUTATED	43	54.4 (12.1)
20P GAIN WILD-TYPE	468	41.9 (13.0)

Figure S57. Get High-res Image Gene #35: '20p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'20p gain' versus 'RADIATION_THERAPY'

P value = 0.0401 (Fisher's exact test), Q value = 0.2

Table S58. Gene #35: '20p gain' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	184	293
20P GAIN MUTATED	9	30
20P GAIN WILD-TYPE	175	263

Figure S58. Get High-res Image Gene #35: '20p gain' versus Clinical Feature #4: 'RADIATION_THERAPY'

'20p gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0124 (Wilcoxon-test), Q value = 0.088

Table S59. Gene #35: '20p gain' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	306	86.6 (12.6)
20P GAIN MUTATED	26	81.2 (14.0)
20P GAIN WILD-TYPE	280	87.1 (12.3)

Figure S59. Get High-res Image Gene #35: '20p gain' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'20q gain' versus 'Time to Death'

P value = 1.17e-12 (logrank test), Q value = 1.5e-10

Table S60. Gene #36: '20q gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	509	121	0.0 - 211.2 (20.8)
20Q GAIN MUTATED	43	21	0.5 - 54.8 (16.2)
20Q GAIN WILD-TYPE	466	100	0.0 - 211.2 (21.8)

Figure S60. Get High-res Image Gene #36: '20q gain' versus Clinical Feature #1: 'Time to Death'

'20q gain' versus 'YEARS_TO_BIRTH'

P value = 2.98e-08 (Wilcoxon-test), Q value = 1.8e-06

Table S61. Gene #36: '20q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	511	43.0 (13.3)
20Q GAIN MUTATED	43	54.4 (12.3)
20Q GAIN WILD-TYPE	468	41.9 (13.0)

Figure S61. Get High-res Image Gene #36: '20q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'20q gain' versus 'RADIATION_THERAPY'

P value = 0.0405 (Fisher's exact test), Q value = 0.2

Table S62. Gene #36: '20q gain' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	184	293
20Q GAIN MUTATED	9	31
20Q GAIN WILD-TYPE	175	262

Figure S62. Get High-res Image Gene #36: '20q gain' versus Clinical Feature #4: 'RADIATION_THERAPY'

'20q gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0124 (Wilcoxon-test), Q value = 0.088

Table S63. Gene #36: '20q gain' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	306	86.6 (12.6)
20Q GAIN MUTATED	26	81.2 (14.0)
20Q GAIN WILD-TYPE	280	87.1 (12.3)

Figure S63. Get High-res Image Gene #36: '20q gain' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'21q gain' versus 'YEARS_TO_BIRTH'

P value = 0.00597 (Wilcoxon-test), Q value = 0.052

Table S64. Gene #37: '21q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	511	43.0 (13.3)
21Q GAIN MUTATED	24	52.0 (17.0)
21Q GAIN WILD-TYPE	487	42.5 (13.0)

Figure S64. 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 S65. 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 S65. Get High-res Image Gene #38: '22q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'22q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00411 (Fisher's exact test), Q value = 0.04

Table S66. 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 S66. Get High-res Image Gene #38: '22q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'xp gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0349 (Fisher's exact test), Q value = 0.18

Table S67. Gene #39: 'xp gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	194	129	189
XP GAIN MUTATED	13	5	3
XP GAIN WILD-TYPE	181	124	186

Figure S67. Get High-res Image Gene #39: 'xp gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'xq gain' versus 'YEARS_TO_BIRTH'

P value = 0.0496 (Wilcoxon-test), Q value = 0.22

Table S68. Gene #40: 'xq gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	511	43.0 (13.3)
XQ GAIN MUTATED	39	39.4 (12.3)
XQ GAIN WILD-TYPE	472	43.3 (13.4)

Figure S68. Get High-res Image Gene #40: 'xq gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'xq gain' versus 'GENDER'

P value = 0.0043 (Fisher's exact test), Q value = 0.042

Table S69. Gene #40: 'xq gain' versus Clinical Feature #3: 'GENDER'

nPatients	FEMALE	MALE
ALL	228	284
XQ GAIN MUTATED	26	13
XQ GAIN WILD-TYPE	202	271

Figure S69. Get High-res Image Gene #40: 'xq gain' versus Clinical Feature #3: 'GENDER'

'xq gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00743 (Fisher's exact test), Q value = 0.059

Table S70. Gene #40: 'xq gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	194	129	189
XQ GAIN MUTATED	18	15	6
XQ GAIN WILD-TYPE	176	114	183

Figure S70. Get High-res Image Gene #40: 'xq gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'xq gain' versus 'ETHNICITY'

P value = 0.0194 (Fisher's exact test), Q value = 0.12

Table S71. Gene #40: 'xq gain' versus Clinical Feature #8: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	32	446
XQ GAIN MUTATED	6	28
XQ GAIN WILD-TYPE	26	418

Figure S71. Get High-res Image Gene #40: 'xq gain' versus Clinical Feature #8: 'ETHNICITY'

'1p loss' versus 'Time to Death'

P value = 9.05e-05 (logrank test), Q value = 0.0019

Table S72. Gene #41: '1p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	509	121	0.0 - 211.2 (20.8)
1P LOSS MUTATED	182	26	0.1 - 182.3 (22.2)
1P LOSS WILD-TYPE	327	95	0.0 - 211.2 (20.2)

Figure S72. Get High-res Image Gene #41: '1p loss' versus Clinical Feature #1: 'Time to Death'

'1p loss' versus 'YEARS_TO_BIRTH'

P value = 0.00101 (Wilcoxon-test), Q value = 0.013

Table S73. 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 S73. Get High-res Image Gene #41: '1p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'1p loss' versus 'RADIATION_THERAPY'

P value = 5.62e-08 (Fisher's exact test), Q value = 3e-06

Table S74. Gene #41: '1p loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	184	293
1P LOSS MUTATED	94	77
1P LOSS WILD-TYPE	90	216

Figure S74. 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 = 0.00027

Table S75. Gene #41: '1p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	194	129	189
1P LOSS MUTATED	10	39	135
1P LOSS WILD-TYPE	184	90	54

Figure S75. Get High-res Image Gene #41: '1p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'1q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0045 (Fisher's exact test), Q value = 0.042

Table S76. Gene #42: '1q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	194	129	189
1Q LOSS MUTATED	4	4	17
1Q LOSS WILD-TYPE	190	125	172

Figure S76. 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 = 0.093

Table S77. Gene #43: '2p loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	184	293
2P LOSS MUTATED	2	17
2P LOSS WILD-TYPE	182	276

Figure S77. Get High-res Image Gene #43: '2p loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

'2q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0492 (Fisher's exact test), Q value = 0.22

Table S78. 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 S78. Get High-res Image Gene #44: '2q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'3p loss' versus 'Time to Death'

P value = 0.0466 (logrank test), Q value = 0.22

Table S79. Gene #45: '3p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	509	121	0.0 - 211.2 (20.8)
3P LOSS MUTATED	29	11	0.1 - 84.3 (24.3)
3P LOSS WILD-TYPE	480	110	0.0 - 211.2 (20.7)

Figure S79. Get High-res Image Gene #45: '3p loss' versus Clinical Feature #1: 'Time to Death'

'3p loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00198 (Wilcoxon-test), Q value = 0.023

Table S80. Gene #45: '3p loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	306	86.6 (12.6)
3P LOSS MUTATED	21	78.6 (13.9)
3P LOSS WILD-TYPE	285	87.2 (12.3)

Figure S80. Get High-res Image Gene #45: '3p loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'3q loss' versus 'Time to Death'

P value = 0.0245 (logrank test), Q value = 0.15

Table S81. Gene #46: '3q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	509	121	0.0 - 211.2 (20.8)
3Q LOSS MUTATED	28	13	0.0 - 117.4 (24.2)
3Q LOSS WILD-TYPE	481	108	0.1 - 211.2 (20.7)

Figure S81. Get High-res Image Gene #46: '3q loss' versus Clinical Feature #1: 'Time to Death'

'4p loss' versus 'YEARS_TO_BIRTH'

P value = 0.00404 (Wilcoxon-test), Q value = 0.04

Table S82. Gene #47: '4p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	511	43.0 (13.3)
4P LOSS MUTATED	71	47.0 (12.5)
4P LOSS WILD-TYPE	440	42.3 (13.4)

Figure S82. Get High-res Image Gene #47: '4p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'4p loss' versus 'GENDER'

P value = 0.0542 (Fisher's exact test), Q value = 0.24

Table S83. Gene #47: '4p loss' versus Clinical Feature #3: 'GENDER'

nPatients	FEMALE	MALE
ALL	228	284
4P LOSS MUTATED	24	47
4P LOSS WILD-TYPE	204	237

Figure S83. Get High-res Image Gene #47: '4p loss' versus Clinical Feature #3: 'GENDER'

'4p loss' versus 'HISTOLOGICAL_TYPE'

P value = 3e-04 (Fisher's exact test), Q value = 0.0051

Table S84. Gene #47: '4p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	194	129	189
4P LOSS MUTATED	13	19	39
4P LOSS WILD-TYPE	181	110	150

Figure S84. Get High-res Image Gene #47: '4p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'4q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00617 (Fisher's exact test), Q value = 0.053

Table S85. Gene #48: '4q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	194	129	189
4Q LOSS MUTATED	23	23	46
4Q LOSS WILD-TYPE	171	106	143

Figure S85. Get High-res Image Gene #48: '4q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'5p loss' versus 'RADIATION_THERAPY'

P value = 0.00728 (Fisher's exact test), Q value = 0.058

Table S86. Gene #49: '5p loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	184	293
5P LOSS MUTATED	5	26
5P LOSS WILD-TYPE	179	267

Figure S86. Get High-res Image Gene #49: '5p loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

'5p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0139 (Fisher's exact test), Q value = 0.093

Table S87. Gene #49: '5p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	194	129	189
5P LOSS MUTATED	18	11	5
5P LOSS WILD-TYPE	176	118	184

Figure S87. Get High-res Image Gene #49: '5p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'5q loss' versus 'RADIATION_THERAPY'

P value = 0.00311 (Fisher's exact test), Q value = 0.034

Table S88. Gene #50: '5q loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	184	293
5Q LOSS MUTATED	4	26
5Q LOSS WILD-TYPE	180	267

Figure S88. Get High-res Image Gene #50: '5q loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

'5q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0247 (Fisher's exact test), Q value = 0.15

Table S89. Gene #50: '5q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	194	129	189
5Q LOSS MUTATED	20	6	7
5Q LOSS WILD-TYPE	174	123	182

Figure S89. Get High-res Image Gene #50: '5q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'6p loss' versus 'Time to Death'

P value = 8.3e-05 (logrank test), Q value = 0.0019

Table S90. Gene #51: '6p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	509	121	0.0 - 211.2 (20.8)
6P LOSS MUTATED	30	13	0.2 - 65.4 (19.3)
6P LOSS WILD-TYPE	479	108	0.0 - 211.2 (21.0)

Figure S90. 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 S91. 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 S91. Get High-res Image Gene #51: '6p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'6p loss' versus 'RADIATION_THERAPY'

P value = 0.0578 (Fisher's exact test), Q value = 0.25

Table S92. Gene #51: '6p loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	184	293
6P LOSS MUTATED	5	20
6P LOSS WILD-TYPE	179	273

Figure S92. Get High-res Image Gene #51: '6p loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

'6q loss' versus 'Time to Death'

P value = 1.96e-05 (logrank test), Q value = 0.00049

Table S93. Gene #52: '6q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	509	121	0.0 - 211.2 (20.8)
6Q LOSS MUTATED	61	20	0.1 - 65.4 (17.9)
6Q LOSS WILD-TYPE	448	101	0.0 - 211.2 (21.8)

Figure S93. 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 S94. 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 S94. Get High-res Image Gene #52: '6q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'6q loss' versus 'RADIATION_THERAPY'

P value = 0.0256 (Fisher's exact test), Q value = 0.15

Table S95. Gene #52: '6q loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	184	293
6Q LOSS MUTATED	13	40
6Q LOSS WILD-TYPE	171	253

Figure S95. Get High-res Image Gene #52: '6q loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

'6q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.000617 (Wilcoxon-test), Q value = 0.0095

Table S96. Gene #52: '6q loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	306	86.6 (12.6)
6Q LOSS MUTATED	40	80.8 (12.9)
6Q LOSS WILD-TYPE	266	87.5 (12.3)

Figure S96. Get High-res Image Gene #52: '6q loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'6q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00136 (Fisher's exact test), Q value = 0.017

Table S97. 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 S97. Get High-res Image Gene #52: '6q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'6q loss' versus 'RACE'

P value = 0.0512 (Fisher's exact test), Q value = 0.23

Table S98. 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 S98. Get High-res Image Gene #52: '6q loss' versus Clinical Feature #7: 'RACE'

'8p loss' versus 'Time to Death'

P value = 0.045 (logrank test), Q value = 0.21

Table S99. Gene #55: '8p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	509	121	0.0 - 211.2 (20.8)
8P LOSS MUTATED	16	6	0.2 - 51.9 (19.9)
8P LOSS WILD-TYPE	493	115	0.0 - 211.2 (21.0)

Figure S99. Get High-res Image Gene #55: '8p loss' versus Clinical Feature #1: 'Time to Death'

'8q loss' versus 'Time to Death'

P value = 0.0438 (logrank test), Q value = 0.21

Table S100. Gene #56: '8q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	509	121	0.0 - 211.2 (20.8)
8Q LOSS MUTATED	11	4	0.2 - 51.9 (19.1)
8Q LOSS WILD-TYPE	498	117	0.0 - 211.2 (21.2)

Figure S100. Get High-res Image Gene #56: '8q loss' versus Clinical Feature #1: 'Time to Death'

'9p loss' versus 'Time to Death'

P value = 3.1e-06 (logrank test), Q value = 0.00011

Table S101. Gene #57: '9p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	509	121	0.0 - 211.2 (20.8)
9P LOSS MUTATED	116	44	0.1 - 169.8 (20.4)
9P LOSS WILD-TYPE	393	77	0.0 - 211.2 (21.3)

Figure S101. 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 = 0.023

Table S102. 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 S102. Get High-res Image Gene #57: '9p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'9p loss' versus 'RADIATION_THERAPY'

P value = 0.000963 (Fisher's exact test), Q value = 0.013

Table S103. Gene #57: '9p loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	184	293
9P LOSS MUTATED	26	79
9P LOSS WILD-TYPE	158	214

Figure S103. Get High-res Image Gene #57: '9p loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

'9p loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0022 (Wilcoxon-test), Q value = 0.025

Table S104. Gene #57: '9p loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	306	86.6 (12.6)
9P LOSS MUTATED	75	83.1 (13.0)
9P LOSS WILD-TYPE	231	87.8 (12.2)

Figure S104. Get High-res Image Gene #57: '9p loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'9p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0582 (Fisher's exact test), Q value = 0.25

Table S105. 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 S105. Get High-res Image Gene #57: '9p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'9q loss' versus 'Time to Death'

P value = 0.00858 (logrank test), Q value = 0.065

Table S106. Gene #58: '9q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	509	121	0.0 - 211.2 (20.8)
9Q LOSS MUTATED	50	20	0.1 - 169.8 (21.6)
9Q LOSS WILD-TYPE	459	101	0.0 - 211.2 (20.8)

Figure S106. 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 = 0.052

Table S107. 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 S107. 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 = 0.08

Table S108. Gene #58: '9q loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	184	293
9Q LOSS MUTATED	8	33
9Q LOSS WILD-TYPE	176	260

Figure S108. Get High-res Image Gene #58: '9q loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

'9q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.000384 (Wilcoxon-test), Q value = 0.0064

Table S109. Gene #58: '9q loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	306	86.6 (12.6)
9Q LOSS MUTATED	32	80.0 (12.2)
9Q LOSS WILD-TYPE	274	87.4 (12.4)

Figure S109. 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 S110. Gene #59: '10p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	509	121	0.0 - 211.2 (20.8)
10P LOSS MUTATED	83	48	0.1 - 134.3 (16.2)
10P LOSS WILD-TYPE	426	73	0.0 - 211.2 (23.5)

Figure S110. 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 S111. 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 S111. Get High-res Image Gene #59: '10p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'10p loss' versus 'RADIATION_THERAPY'

P value = 0.000138 (Fisher's exact test), Q value = 0.0027

Table S112. Gene #59: '10p loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	184	293
10P LOSS MUTATED	14	60
10P LOSS WILD-TYPE	170	233

Figure S112. Get High-res Image Gene #59: '10p loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

'10p loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.000218 (Wilcoxon-test), Q value = 0.0039

Table S113. Gene #59: '10p loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	306	86.6 (12.6)
10P LOSS MUTATED	52	80.4 (14.9)
10P LOSS WILD-TYPE	254	87.9 (11.7)

Figure S113. Get High-res Image Gene #59: '10p loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'10p loss' versus 'HISTOLOGICAL_TYPE'

P value = 9e-05 (Fisher's exact test), Q value = 0.0019

Table S114. 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 S114. Get High-res Image Gene #59: '10p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'10p loss' versus 'RACE'

P value = 0.00884 (Fisher's exact test), Q value = 0.067

Table S115. 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 S115. 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 S116. Gene #60: '10q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	509	121	0.0 - 211.2 (20.8)
10Q LOSS MUTATED	96	54	0.1 - 172.8 (16.5)
10Q LOSS WILD-TYPE	413	67	0.0 - 211.2 (23.5)

Figure S116. Get High-res Image Gene #60: '10q loss' versus Clinical Feature #1: 'Time to Death'

'10q loss' versus 'YEARS_TO_BIRTH'

P value = 2.03e-17 (Wilcoxon-test), Q value = 3.3e-15

Table S117. Gene #60: '10q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	511	43.0 (13.3)
10Q LOSS MUTATED	96	53.6 (12.3)
10Q LOSS WILD-TYPE	415	40.5 (12.3)

Figure S117. Get High-res Image Gene #60: '10q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'10q loss' versus 'RADIATION_THERAPY'

P value = 4.74e-06 (Fisher's exact test), Q value = 0.00015

Table S118. Gene #60: '10q loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	184	293
10Q LOSS MUTATED	15	71
10Q LOSS WILD-TYPE	169	222

Figure S118. Get High-res Image Gene #60: '10q loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

'10q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.000462 (Wilcoxon-test), Q value = 0.0075

Table S119. Gene #60: '10q loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	306	86.6 (12.6)
10Q LOSS MUTATED	59	81.0 (14.9)
10Q LOSS WILD-TYPE	247	88.0 (11.6)

Figure S119. Get High-res Image Gene #60: '10q loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'10q loss' versus 'HISTOLOGICAL_TYPE'

P value = 4e-05 (Fisher's exact test), Q value = 0.00096

Table S120. Gene #60: '10q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	194	129	189
10Q LOSS MUTATED	56	19	21
10Q LOSS WILD-TYPE	138	110	168

Figure S120. Get High-res Image Gene #60: '10q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'10q loss' versus 'RACE'

P value = 0.0252 (Fisher's exact test), Q value = 0.15

Table S121. 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	85
10Q LOSS WILD-TYPE	0	7	13	387

Figure S121. Get High-res Image Gene #60: '10q loss' versus Clinical Feature #7: 'RACE'

'11p loss' versus 'Time to Death'

P value = 0.0222 (logrank test), Q value = 0.14

Table S122. Gene #61: '11p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	509	121	0.0 - 211.2 (20.8)
11P LOSS MUTATED	63	24	0.2 - 156.2 (20.2)
11P LOSS WILD-TYPE	446	97	0.0 - 211.2 (21.0)

Figure S122. Get High-res Image Gene #61: '11p loss' versus Clinical Feature #1: 'Time to Death'

'11p loss' versus 'RADIATION_THERAPY'

P value = 0.00625 (Fisher's exact test), Q value = 0.053

Table S123. Gene #61: '11p loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	184	293
11P LOSS MUTATED	13	46
11P LOSS WILD-TYPE	171	247

Figure S123. Get High-res Image Gene #61: '11p loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

'11p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00065 (Fisher's exact test), Q value = 0.0098

Table S124. 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 S124. Get High-res Image Gene #61: '11p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'11q loss' versus 'Time to Death'

P value = 9.85e-05 (logrank test), Q value = 0.002

Table S125. Gene #62: '11q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	509	121	0.0 - 211.2 (20.8)
11Q LOSS MUTATED	21	9	0.2 - 54.8 (18.7)
11Q LOSS WILD-TYPE	488	112	0.0 - 211.2 (21.4)

Figure S125. Get High-res Image Gene #62: '11q loss' versus Clinical Feature #1: 'Time to Death'

'11q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0131 (Fisher's exact test), Q value = 0.091

Table S126. 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 S126. Get High-res Image Gene #62: '11q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'12q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00457 (Fisher's exact test), Q value = 0.042

Table S127. Gene #64: '12q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	194	129	189
12Q LOSS MUTATED	28	14	9
12Q LOSS WILD-TYPE	166	115	180

Figure S127. Get High-res Image Gene #64: '12q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'13q loss' versus 'RADIATION_THERAPY'

P value = 0.000824 (Fisher's exact test), Q value = 0.012

Table S128. Gene #65: '13q loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	184	293
13Q LOSS MUTATED	28	84
13Q LOSS WILD-TYPE	156	209

Figure S128. Get High-res Image Gene #65: '13q loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

'14q loss' versus 'Time to Death'

P value = 2.75e-06 (logrank test), Q value = 1e-04

Table S129. Gene #66: '14q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	509	121	0.0 - 211.2 (20.8)
14Q LOSS MUTATED	79	33	0.1 - 130.8 (21.3)
14Q LOSS WILD-TYPE	430	88	0.0 - 211.2 (20.8)

Figure S129. Get High-res Image Gene #66: '14q loss' versus Clinical Feature #1: 'Time to Death'

'14q loss' versus 'YEARS_TO_BIRTH'

P value = 1.66e-05 (Wilcoxon-test), Q value = 0.00043

Table S130. Gene #66: '14q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	511	43.0 (13.3)
14Q LOSS MUTATED	80	49.0 (13.0)
14Q LOSS WILD-TYPE	431	41.9 (13.1)

Figure S130. Get High-res Image Gene #66: '14q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'14q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0339 (Wilcoxon-test), Q value = 0.18

Table S131. Gene #66: '14q loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	306	86.6 (12.6)
14Q LOSS MUTATED	50	83.4 (13.2)
14Q LOSS WILD-TYPE	256	87.3 (12.4)

Figure S131. Get High-res Image Gene #66: '14q loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'16p loss' versus 'Time to Death'

P value = 0.0509 (logrank test), Q value = 0.23

Table S132. Gene #68: '16p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	509	121	0.0 - 211.2 (20.8)
16P LOSS MUTATED	14	7	2.4 - 78.3 (28.6)
16P LOSS WILD-TYPE	495	114	0.0 - 211.2 (20.7)

Figure S132. 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 S133. 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 S133. 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 S134. 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 S134. Get High-res Image Gene #69: '16q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'16q loss' versus 'RADIATION_THERAPY'

P value = 0.021 (Fisher's exact test), Q value = 0.13

Table S135. Gene #69: '16q loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	184	293
16Q LOSS MUTATED	3	18
16Q LOSS WILD-TYPE	181	275

Figure S135. Get High-res Image Gene #69: '16q loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

'17p loss' versus 'Time to Death'

P value = 0.0351 (logrank test), Q value = 0.18

Table S136. Gene #70: '17p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	509	121	0.0 - 211.2 (20.8)
17P LOSS MUTATED	13	3	0.1 - 33.3 (15.0)
17P LOSS WILD-TYPE	496	118	0.0 - 211.2 (21.3)

Figure S136. Get High-res Image Gene #70: '17p loss' versus Clinical Feature #1: 'Time to Death'

'17p loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00849 (Wilcoxon-test), Q value = 0.065

Table S137. Gene #70: '17p loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	306	86.6 (12.6)
17P LOSS MUTATED	6	75.0 (8.4)
17P LOSS WILD-TYPE	300	86.9 (12.5)

Figure S137. Get High-res Image Gene #70: '17p loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'17p loss' versus 'ETHNICITY'

P value = 0.0493 (Fisher's exact test), Q value = 0.22

Table S138. Gene #70: '17p loss' versus Clinical Feature #8: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	32	446
17P LOSS MUTATED	3	10
17P LOSS WILD-TYPE	29	436

Figure S138. Get High-res Image Gene #70: '17p loss' versus Clinical Feature #8: 'ETHNICITY'

'18p loss' versus 'YEARS_TO_BIRTH'

P value = 0.002 (Wilcoxon-test), Q value = 0.023

Table S139. Gene #72: '18p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	511	43.0 (13.3)
18P LOSS MUTATED	68	48.1 (14.5)
18P LOSS WILD-TYPE	443	42.2 (13.0)

Figure S139. 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 S140. 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 S140. 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 = 0.18

Table S141. 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 S141. Get High-res Image Gene #73: '18q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'19p loss' versus 'RACE'

P value = 0.0187 (Fisher's exact test), Q value = 0.12

Table S142. 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	19
19P LOSS WILD-TYPE	1	7	17	453

Figure S142. Get High-res Image Gene #74: '19p loss' versus Clinical Feature #7: 'RACE'

'19p loss' versus 'ETHNICITY'

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

Table S143. Gene #74: '19p loss' versus Clinical Feature #8: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	32	446
19P LOSS MUTATED	4	18
19P LOSS WILD-TYPE	28	428

Figure S143. Get High-res Image Gene #74: '19p loss' versus Clinical Feature #8: 'ETHNICITY'

'19q loss' versus 'Time to Death'

P value = 0.00139 (logrank test), Q value = 0.017

Table S144. Gene #75: '19q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	509	121	0.0 - 211.2 (20.8)
19Q LOSS MUTATED	207	36	0.1 - 182.3 (22.4)
19Q LOSS WILD-TYPE	302	85	0.0 - 211.2 (20.1)

Figure S144. 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 S145. 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 S145. Get High-res Image Gene #75: '19q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'19q loss' versus 'RADIATION_THERAPY'

P value = 4.1e-06 (Fisher's exact test), Q value = 0.00014

Table S146. Gene #75: '19q loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	184	293
19Q LOSS MUTATED	100	96
19Q LOSS WILD-TYPE	84	197

Figure S146. 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 = 0.00027

Table S147. 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 S147. Get High-res Image Gene #75: '19q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'20p loss' versus 'RADIATION_THERAPY'

P value = 0.0469 (Fisher's exact test), Q value = 0.22

Table S148. Gene #76: '20p loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	184	293
20P LOSS MUTATED	0	7
20P LOSS WILD-TYPE	184	286

Figure S148. Get High-res Image Gene #76: '20p loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

'21q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00633 (Wilcoxon-test), Q value = 0.053

Table S149. Gene #78: '21q loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	306	86.6 (12.6)
21Q LOSS MUTATED	27	80.4 (14.0)
21Q LOSS WILD-TYPE	279	87.2 (12.3)

Figure S149. Get High-res Image Gene #78: '21q loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'21q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00359 (Fisher's exact test), Q value = 0.037

Table S150. Gene #78: '21q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	194	129	189
21Q LOSS MUTATED	23	7	6
21Q LOSS WILD-TYPE	171	122	183

Figure S150. Get High-res Image Gene #78: '21q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'22q loss' versus 'Time to Death'

P value = 8.53e-08 (logrank test), Q value = 4.3e-06

Table S151. Gene #79: '22q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	509	121	0.0 - 211.2 (20.8)
22Q LOSS MUTATED	57	27	0.1 - 156.2 (19.3)
22Q LOSS WILD-TYPE	452	94	0.0 - 211.2 (21.4)

Figure S151. 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 = 8.3e-05

Table S152. 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 S152. Get High-res Image Gene #79: '22q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'22q loss' versus 'RADIATION_THERAPY'

P value = 0.035 (Fisher's exact test), Q value = 0.18

Table S153. Gene #79: '22q loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	184	293
22Q LOSS MUTATED	13	39
22Q LOSS WILD-TYPE	171	254

Figure S153. Get High-res Image Gene #79: '22q loss' versus Clinical Feature #4: 'RADIATION_THERAPY'

'22q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00527 (Wilcoxon-test), Q value = 0.048

Table S154. Gene #79: '22q loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	306	86.6 (12.6)
22Q LOSS MUTATED	35	80.6 (15.1)
22Q LOSS WILD-TYPE	271	87.4 (12.0)

Figure S154. Get High-res Image Gene #79: '22q loss' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'xq loss' versus 'Time to Death'

P value = 0.00453 (logrank test), Q value = 0.042

Table S155. Gene #81: 'xq loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	509	121	0.0 - 211.2 (20.8)
XQ LOSS MUTATED	70	23	0.1 - 134.3 (18.0)
XQ LOSS WILD-TYPE	439	98	0.0 - 211.2 (22.1)

Figure S155. 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/19781938/transformed.cor.cli.txt
Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/LGG-TP/19775312/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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