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

Glioblastoma Multiforme (Primary solid tumor)

21 August 2015 | analyses__2015_08_21

Maintainer Information

Citation Information

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

Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1QZ296D

Overview

Introduction

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

Summary

Testing the association between copy number variation 82 arm-level events and 8 clinical features across 571 patients, 15 significant findings detected with Q value < 0.25.

7p gain cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.
7q gain cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.
10p gain cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.
20p gain cnv correlated to 'YEARS_TO_BIRTH'.
20q gain cnv correlated to 'YEARS_TO_BIRTH'.
6p loss cnv correlated to 'Time to Death'.
8p loss cnv correlated to 'RACE'.
10p loss cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', and 'HISTOLOGICAL_TYPE'.
10q loss cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 82 arm-level events and 8 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 15 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
10p loss	477 (84%)	94	0.000172 (0.0113)	3.02e-09 (1.98e-06)	0.167 (1.00)	0.612 (1.00)	0.08 (0.874)	0.00512 (0.224)	0.108 (0.948)	0.132 (0.982)
7p gain	463 (81%)	108	3.3e-05 (0.00361)	2.23e-06 (0.000487)	0.743 (1.00)	0.207 (1.00)	0.935 (1.00)	0.0338 (0.813)	0.0539 (0.824)	0.27 (1.00)
7q gain	468 (82%)	103	6.67e-05 (0.00547)	7.76e-06 (0.00127)	0.222 (1.00)	0.518 (1.00)	0.882 (1.00)	0.0362 (0.813)	0.0368 (0.813)	0.249 (1.00)
10p gain	13 (2%)	558	0.00178 (0.0975)	6.15e-05 (0.00547)	0.0403 (0.824)	0.375 (1.00)	0.348 (1.00)	0.286 (1.00)	0.0131 (0.469)	0.281 (1.00)
10q loss	488 (85%)	83	0.000195 (0.0116)	1.32e-07 (4.34e-05)	0.466 (1.00)	1 (1.00)	0.00985 (0.404)	0.0596 (0.855)	0.0777 (0.874)	0.0906 (0.902)
20p gain	220 (39%)	351	0.298 (1.00)	2.5e-05 (0.00328)	0.333 (1.00)	0.898 (1.00)	0.86 (1.00)	0.465 (1.00)	0.0372 (0.813)	1 (1.00)
20q gain	218 (38%)	353	0.516 (1.00)	0.00013 (0.00951)	0.29 (1.00)	1 (1.00)	0.781 (1.00)	0.478 (1.00)	0.0535 (0.824)	1 (1.00)
6p loss	86 (15%)	485	0.00326 (0.164)	0.383 (1.00)	0.811 (1.00)	0.165 (1.00)	0.692 (1.00)	0.602 (1.00)	0.256 (1.00)	0.702 (1.00)
8p loss	58 (10%)	513	0.725 (1.00)	0.173 (1.00)	0.156 (1.00)	0.68 (1.00)	0.42 (1.00)	0.569 (1.00)	0.00395 (0.185)	0.619 (1.00)
1p gain	81 (14%)	490	0.315 (1.00)	0.464 (1.00)	0.624 (1.00)	0.156 (1.00)	0.119 (0.951)	0.0279 (0.733)	0.852 (1.00)	0.664 (1.00)
1q gain	88 (15%)	483	0.848 (1.00)	0.611 (1.00)	0.288 (1.00)	0.228 (1.00)	0.274 (1.00)	0.199 (1.00)	0.774 (1.00)	0.687 (1.00)
2p gain	37 (6%)	534	0.545 (1.00)	0.781 (1.00)	0.121 (0.954)	0.452 (1.00)	0.351 (1.00)	1 (1.00)	0.339 (1.00)	1 (1.00)
2q gain	36 (6%)	535	0.37 (1.00)	0.309 (1.00)	0.378 (1.00)	0.796 (1.00)	0.236 (1.00)	1 (1.00)	0.325 (1.00)	1 (1.00)
3p gain	57 (10%)	514	0.773 (1.00)	0.0444 (0.824)	0.319 (1.00)	0.538 (1.00)	0.606 (1.00)	0.611 (1.00)	0.927 (1.00)	1 (1.00)
3q gain	63 (11%)	508	0.635 (1.00)	0.111 (0.948)	0.412 (1.00)	0.843 (1.00)	0.551 (1.00)	0.47 (1.00)	0.932 (1.00)	1 (1.00)
4p gain	36 (6%)	535	0.752 (1.00)	0.495 (1.00)	0.86 (1.00)	0.796 (1.00)	0.0472 (0.824)	1 (1.00)	0.571 (1.00)	0.575 (1.00)
4q gain	33 (6%)	538	0.948 (1.00)	0.567 (1.00)	0.467 (1.00)	1 (1.00)	0.044 (0.824)	1 (1.00)	0.532 (1.00)	1 (1.00)
5p gain	49 (9%)	522	0.697 (1.00)	0.688 (1.00)	0.169 (1.00)	0.376 (1.00)	0.206 (1.00)	0.0664 (0.855)	1 (1.00)	0.298 (1.00)
5q gain	41 (7%)	530	0.361 (1.00)	0.524 (1.00)	0.134 (0.982)	0.213 (1.00)	0.719 (1.00)	0.113 (0.948)	0.913 (1.00)	0.612 (1.00)
6p gain	24 (4%)	547	0.255 (1.00)	0.498 (1.00)	0.671 (1.00)	1 (1.00)	0.787 (1.00)	1 (1.00)	0.483 (1.00)	1 (1.00)
6q gain	23 (4%)	548	0.195 (1.00)	0.25 (1.00)	1 (1.00)	1 (1.00)	0.751 (1.00)	1 (1.00)	0.562 (1.00)	1 (1.00)
8p gain	52 (9%)	519	0.879 (1.00)	0.814 (1.00)	0.657 (1.00)	0.376 (1.00)	0.74 (1.00)	0.635 (1.00)	0.32 (1.00)	1 (1.00)
8q gain	59 (10%)	512	0.473 (1.00)	0.373 (1.00)	0.482 (1.00)	0.675 (1.00)	0.844 (1.00)	0.49 (1.00)	0.762 (1.00)	1 (1.00)
9p gain	47 (8%)	524	0.335 (1.00)	0.642 (1.00)	0.163 (1.00)	0.356 (1.00)	0.898 (1.00)	0.145 (0.991)	0.297 (1.00)	0.24 (1.00)
9q gain	70 (12%)	501	0.926 (1.00)	0.926 (1.00)	0.153 (1.00)	0.131 (0.982)	0.791 (1.00)	0.333 (1.00)	0.297 (1.00)	0.644 (1.00)
10q gain	3 (1%)	568	0.341 (1.00)	0.661 (1.00)	0.564 (1.00)	1 (1.00)		1 (1.00)	1 (1.00)	0.0726 (0.855)
11p gain	17 (3%)	554	0.619 (1.00)	0.96 (1.00)	0.806 (1.00)	0.715 (1.00)	0.431 (1.00)	1 (1.00)	0.598 (1.00)	0.335 (1.00)
11q gain	14 (2%)	557	0.275 (1.00)	0.117 (0.951)	0.267 (1.00)	0.705 (1.00)	0.169 (1.00)	0.463 (1.00)	1 (1.00)	0.299 (1.00)
12p gain	59 (10%)	512	0.608 (1.00)	0.31 (1.00)	0.482 (1.00)	0.0637 (0.855)	0.438 (1.00)	0.791 (1.00)	0.928 (1.00)	1 (1.00)
12q gain	48 (8%)	523	0.999 (1.00)	0.617 (1.00)	0.218 (1.00)	0.18 (1.00)	0.659 (1.00)	0.56 (1.00)	0.142 (0.991)	0.612 (1.00)
13q gain	10 (2%)	561	0.434 (1.00)	0.0108 (0.419)	0.201 (1.00)	0.295 (1.00)	0.0846 (0.89)	0.571 (1.00)	1 (1.00)	1 (1.00)
14q gain	22 (4%)	549	0.269 (1.00)	0.058 (0.855)	0.513 (1.00)	0.743 (1.00)	0.494 (1.00)	0.0771 (0.874)	0.829 (1.00)	1 (1.00)
15q gain	24 (4%)	547	0.272 (1.00)	0.878 (1.00)	0.526 (1.00)	0.118 (0.951)	0.108 (0.948)	0.828 (1.00)	0.841 (1.00)	1 (1.00)
16p gain	38 (7%)	533	0.0464 (0.824)	0.858 (1.00)	0.305 (1.00)	0.456 (1.00)	0.99 (1.00)	1 (1.00)	0.462 (1.00)	1 (1.00)
16q gain	37 (6%)	534	0.178 (1.00)	0.88 (1.00)	0.606 (1.00)	0.455 (1.00)	0.881 (1.00)	1 (1.00)	0.453 (1.00)	1 (1.00)
17p gain	48 (8%)	523	0.101 (0.948)	0.0254 (0.718)	0.281 (1.00)	0.177 (1.00)	0.574 (1.00)	0.46 (1.00)	0.411 (1.00)	1 (1.00)
17q gain	59 (10%)	512	0.0212 (0.661)	0.0136 (0.469)	0.576 (1.00)	0.153 (1.00)	0.659 (1.00)	0.67 (1.00)	0.534 (1.00)	0.375 (1.00)
18p gain	57 (10%)	514	0.55 (1.00)	0.392 (1.00)	0.669 (1.00)	0.835 (1.00)	0.477 (1.00)	0.07 (0.855)	0.205 (1.00)	0.346 (1.00)
18q gain	57 (10%)	514	0.672 (1.00)	0.228 (1.00)	0.2 (1.00)	0.835 (1.00)	0.376 (1.00)	0.0707 (0.855)	0.399 (1.00)	1 (1.00)
19p gain	223 (39%)	348	0.51 (1.00)	0.947 (1.00)	0.793 (1.00)	0.0956 (0.936)	0.872 (1.00)	0.54 (1.00)	0.497 (1.00)	0.552 (1.00)
19q gain	197 (35%)	374	0.641 (1.00)	0.473 (1.00)	0.653 (1.00)	0.6 (1.00)	0.732 (1.00)	0.751 (1.00)	0.262 (1.00)	0.357 (1.00)
21q gain	63 (11%)	508	0.71 (1.00)	0.0818 (0.88)	0.892 (1.00)	0.842 (1.00)	0.506 (1.00)	0.178 (1.00)	0.109 (0.948)	0.376 (1.00)
22q gain	34 (6%)	537	0.225 (1.00)	0.571 (1.00)	1 (1.00)	0.603 (1.00)	0.346 (1.00)	0.328 (1.00)	0.794 (1.00)	0.148 (1.00)
xp gain	15 (3%)	556	0.999 (1.00)	0.439 (1.00)	0.597 (1.00)	0.705 (1.00)	0.546 (1.00)	0.721 (1.00)	0.723 (1.00)	0.203 (1.00)
xq gain	16 (3%)	555	0.427 (1.00)	0.559 (1.00)	1 (1.00)	0.705 (1.00)	0.71 (1.00)	0.373 (1.00)	0.737 (1.00)	0.243 (1.00)
1p loss	15 (3%)	556	0.432 (1.00)	0.0513 (0.824)	0.425 (1.00)	0.44 (1.00)	0.348 (1.00)	0.491 (1.00)	0.737 (1.00)	1 (1.00)
1q loss	14 (2%)	557	0.311 (1.00)	0.0263 (0.718)	1 (1.00)	0.418 (1.00)	0.036 (0.813)	1 (1.00)	0.714 (1.00)	1 (1.00)
2p loss	32 (6%)	539	0.683 (1.00)	0.0792 (0.874)	0.135 (0.982)	0.054 (0.824)	0.863 (1.00)	0.758 (1.00)	0.89 (1.00)	1 (1.00)
2q loss	32 (6%)	539	0.872 (1.00)	0.106 (0.948)	0.263 (1.00)	0.054 (0.824)	0.595 (1.00)	0.352 (1.00)	0.89 (1.00)	1 (1.00)
3p loss	40 (7%)	531	0.505 (1.00)	0.0693 (0.855)	1 (1.00)	0.0457 (0.824)	0.981 (1.00)	0.574 (1.00)	0.744 (1.00)	0.203 (1.00)
3q loss	34 (6%)	537	0.969 (1.00)	0.656 (1.00)	0.589 (1.00)	0.413 (1.00)	0.629 (1.00)	0.878 (1.00)	0.805 (1.00)	0.514 (1.00)
4p loss	54 (9%)	517	0.227 (1.00)	0.764 (1.00)	0.144 (0.991)	0.395 (1.00)	0.42 (1.00)	0.463 (1.00)	0.644 (1.00)	0.308 (1.00)
4q loss	55 (10%)	516	0.0207 (0.661)	0.135 (0.982)	0.772 (1.00)	0.403 (1.00)	0.583 (1.00)	0.921 (1.00)	0.477 (1.00)	0.288 (1.00)
5p loss	43 (8%)	528	0.108 (0.948)	0.551 (1.00)	0.872 (1.00)	0.34 (1.00)	0.529 (1.00)	0.898 (1.00)	0.0901 (0.902)	0.212 (1.00)
5q loss	44 (8%)	527	0.116 (0.951)	0.602 (1.00)	1 (1.00)	0.34 (1.00)	0.705 (1.00)	0.534 (1.00)	0.315 (1.00)	0.0519 (0.824)
6q loss	124 (22%)	447	0.23 (1.00)	0.756 (1.00)	0.299 (1.00)	0.45 (1.00)	0.856 (1.00)	0.741 (1.00)	0.238 (1.00)	0.476 (1.00)
7p loss	8 (1%)	563	0.471 (1.00)	0.0526 (0.824)	1 (1.00)	1 (1.00)	0.735 (1.00)	1 (1.00)	0.625 (1.00)	1 (1.00)
7q loss	6 (1%)	565	0.628 (1.00)	0.0239 (0.711)	1 (1.00)	0.583 (1.00)	0.309 (1.00)	1 (1.00)	0.521 (1.00)	1 (1.00)
8q loss	42 (7%)	529	0.0607 (0.855)	0.21 (1.00)	0.416 (1.00)	0.635 (1.00)	0.276 (1.00)	0.894 (1.00)	0.286 (1.00)	1 (1.00)
9p loss	199 (35%)	372	0.359 (1.00)	0.574 (1.00)	0.787 (1.00)	0.602 (1.00)	0.724 (1.00)	0.881 (1.00)	0.46 (1.00)	0.064 (0.855)
9q loss	94 (16%)	477	0.786 (1.00)	0.705 (1.00)	0.489 (1.00)	0.396 (1.00)	0.53 (1.00)	0.164 (1.00)	0.133 (0.982)	0.236 (1.00)
11p loss	99 (17%)	472	0.273 (1.00)	0.82 (1.00)	0.0705 (0.855)	1 (1.00)	0.429 (1.00)	0.443 (1.00)	0.698 (1.00)	0.7 (1.00)
11q loss	93 (16%)	478	0.853 (1.00)	0.357 (1.00)	0.419 (1.00)	0.614 (1.00)	0.661 (1.00)	0.806 (1.00)	0.953 (1.00)	0.229 (1.00)
12p loss	58 (10%)	513	0.781 (1.00)	0.612 (1.00)	0.48 (1.00)	0.532 (1.00)	0.97 (1.00)	0.616 (1.00)	0.194 (1.00)	1 (1.00)
12q loss	57 (10%)	514	0.955 (1.00)	0.658 (1.00)	0.568 (1.00)	0.287 (1.00)	0.935 (1.00)	0.368 (1.00)	0.206 (1.00)	0.327 (1.00)
13q loss	185 (32%)	386	0.824 (1.00)	0.805 (1.00)	0.927 (1.00)	0.0855 (0.89)	0.917 (1.00)	0.608 (1.00)	0.537 (1.00)	0.759 (1.00)
14q loss	145 (25%)	426	0.852 (1.00)	0.797 (1.00)	0.326 (1.00)	0.199 (1.00)	0.961 (1.00)	0.498 (1.00)	0.31 (1.00)	0.31 (1.00)
15q loss	106 (19%)	465	0.864 (1.00)	0.073 (0.855)	0.659 (1.00)	0.333 (1.00)	0.766 (1.00)	0.508 (1.00)	1 (1.00)	0.257 (1.00)
16p loss	63 (11%)	508	0.0987 (0.948)	0.309 (1.00)	0.683 (1.00)	0.415 (1.00)	0.433 (1.00)	0.152 (1.00)	1 (1.00)	1 (1.00)
16q loss	82 (14%)	489	0.166 (1.00)	0.834 (1.00)	1 (1.00)	0.368 (1.00)	0.627 (1.00)	0.377 (1.00)	0.684 (1.00)	0.695 (1.00)
17p loss	63 (11%)	508	0.748 (1.00)	0.493 (1.00)	0.412 (1.00)	0.557 (1.00)	0.99 (1.00)	0.93 (1.00)	1 (1.00)	1 (1.00)
17q loss	40 (7%)	531	0.705 (1.00)	0.468 (1.00)	0.502 (1.00)	0.809 (1.00)	0.79 (1.00)	0.893 (1.00)	0.61 (1.00)	0.586 (1.00)
18p loss	71 (12%)	500	0.221 (1.00)	0.859 (1.00)	0.517 (1.00)	0.182 (1.00)	0.345 (1.00)	0.468 (1.00)	0.233 (1.00)	0.65 (1.00)
18q loss	62 (11%)	509	0.536 (1.00)	0.789 (1.00)	0.784 (1.00)	0.0688 (0.855)	0.306 (1.00)	0.68 (1.00)	0.192 (1.00)	0.145 (0.991)
19p loss	27 (5%)	544	0.706 (1.00)	0.949 (1.00)	0.843 (1.00)	0.344 (1.00)	0.509 (1.00)	0.852 (1.00)	1 (1.00)	1 (1.00)
19q loss	35 (6%)	536	0.779 (1.00)	0.879 (1.00)	1 (1.00)	0.413 (1.00)	0.803 (1.00)	0.397 (1.00)	0.712 (1.00)	1 (1.00)
20p loss	19 (3%)	552	0.892 (1.00)	0.426 (1.00)	0.239 (1.00)	0.732 (1.00)	0.661 (1.00)	1 (1.00)	0.2 (1.00)	0.352 (1.00)
20q loss	17 (3%)	554	0.767 (1.00)	0.767 (1.00)	0.313 (1.00)	0.491 (1.00)	0.719 (1.00)	0.764 (1.00)	0.378 (1.00)	1 (1.00)
21q loss	42 (7%)	529	0.518 (1.00)	0.667 (1.00)	0.416 (1.00)	1 (1.00)	0.109 (0.948)	1 (1.00)	1 (1.00)	0.24 (1.00)
22q loss	181 (32%)	390	0.926 (1.00)	0.0908 (0.902)	0.927 (1.00)	0.504 (1.00)	0.384 (1.00)	0.848 (1.00)	0.654 (1.00)	1 (1.00)
xp loss	114 (20%)	457	0.139 (0.991)	0.596 (1.00)	0.391 (1.00)	0.275 (1.00)	0.56 (1.00)	0.873 (1.00)	0.112 (0.948)	0.715 (1.00)
xq loss	106 (19%)	465	0.122 (0.954)	0.63 (1.00)	0.378 (1.00)	0.196 (1.00)	0.511 (1.00)	0.714 (1.00)	0.139 (0.991)	0.473 (1.00)

'7p gain' versus 'Time to Death'

P value = 3.3e-05 (logrank test), Q value = 0.0036

Table S1. Gene #13: '7p gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	570	470	0.1 - 127.6 (12.2)
7P GAIN MUTATED	462	390	0.1 - 127.6 (11.8)
7P GAIN WILD-TYPE	108	80	0.2 - 120.6 (15.2)

Figure S1. Get High-res Image Gene #13: '7p gain' versus Clinical Feature #1: 'Time to Death'

'7p gain' versus 'YEARS_TO_BIRTH'

P value = 2.23e-06 (Wilcoxon-test), Q value = 0.00049

Table S2. Gene #13: '7p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	571	57.7 (14.5)
7P GAIN MUTATED	463	59.6 (12.4)
7P GAIN WILD-TYPE	108	49.6 (19.4)

Figure S2. Get High-res Image Gene #13: '7p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'7q gain' versus 'Time to Death'

P value = 6.67e-05 (logrank test), Q value = 0.0055

Table S3. Gene #14: '7q gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	570	470	0.1 - 127.6 (12.2)
7Q GAIN MUTATED	467	391	0.1 - 127.6 (11.8)
7Q GAIN WILD-TYPE	103	79	0.2 - 120.6 (15.9)

Figure S3. Get High-res Image Gene #14: '7q gain' versus Clinical Feature #1: 'Time to Death'

'7q gain' versus 'YEARS_TO_BIRTH'

P value = 7.76e-06 (Wilcoxon-test), Q value = 0.0013

Table S4. Gene #14: '7q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	571	57.7 (14.5)
7Q GAIN MUTATED	468	59.6 (12.2)
7Q GAIN WILD-TYPE	103	49.4 (20.1)

Figure S4. Get High-res Image Gene #14: '7q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'10p gain' versus 'Time to Death'

P value = 0.00178 (logrank test), Q value = 0.097

Table S5. Gene #19: '10p gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	570	470	0.1 - 127.6 (12.2)
10P GAIN MUTATED	13	8	0.4 - 100.0 (28.7)
10P GAIN WILD-TYPE	557	462	0.1 - 127.6 (12.1)

Figure S5. Get High-res Image Gene #19: '10p gain' versus Clinical Feature #1: 'Time to Death'

'10p gain' versus 'YEARS_TO_BIRTH'

P value = 6.15e-05 (Wilcoxon-test), Q value = 0.0055

Table S6. Gene #19: '10p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	571	57.7 (14.5)
10P GAIN MUTATED	13	37.5 (17.4)
10P GAIN WILD-TYPE	558	58.2 (14.1)

Figure S6. Get High-res Image Gene #19: '10p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'20p gain' versus 'YEARS_TO_BIRTH'

P value = 2.5e-05 (Wilcoxon-test), Q value = 0.0033

Table S7. Gene #36: '20p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	571	57.7 (14.5)
20P GAIN MUTATED	220	61.0 (13.0)
20P GAIN WILD-TYPE	351	55.7 (15.0)

Figure S7. Get High-res Image Gene #36: '20p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'20q gain' versus 'YEARS_TO_BIRTH'

P value = 0.00013 (Wilcoxon-test), Q value = 0.0095

Table S8. Gene #37: '20q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	571	57.7 (14.5)
20Q GAIN MUTATED	218	60.8 (13.3)
20Q GAIN WILD-TYPE	353	55.9 (14.9)

Figure S8. Get High-res Image Gene #37: '20q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'6p loss' versus 'Time to Death'

P value = 0.00326 (logrank test), Q value = 0.16

Table S9. Gene #52: '6p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	570	470	0.1 - 127.6 (12.2)
6P LOSS MUTATED	86	76	0.2 - 92.7 (9.5)
6P LOSS WILD-TYPE	484	394	0.1 - 127.6 (12.6)

Figure S9. Get High-res Image Gene #52: '6p loss' versus Clinical Feature #1: 'Time to Death'

'8p loss' versus 'RACE'

P value = 0.00395 (Fisher's exact test), Q value = 0.19

Table S10. Gene #56: '8p loss' versus Clinical Feature #7: 'RACE'

nPatients	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	13	50	485
8P LOSS MUTATED	5	2	46
8P LOSS WILD-TYPE	8	48	439

Figure S10. Get High-res Image Gene #56: '8p loss' versus Clinical Feature #7: 'RACE'

'10p loss' versus 'Time to Death'

P value = 0.000172 (logrank test), Q value = 0.011

Table S11. Gene #60: '10p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	570	470	0.1 - 127.6 (12.2)
10P LOSS MUTATED	476	399	0.1 - 127.6 (11.9)
10P LOSS WILD-TYPE	94	71	0.4 - 115.9 (14.6)

Figure S11. Get High-res Image Gene #60: '10p loss' versus Clinical Feature #1: 'Time to Death'

'10p loss' versus 'YEARS_TO_BIRTH'

P value = 3.02e-09 (Wilcoxon-test), Q value = 2e-06

Table S12. Gene #60: '10p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	571	57.7 (14.5)
10P LOSS MUTATED	477	59.7 (12.6)
10P LOSS WILD-TYPE	94	47.9 (18.8)

Figure S12. Get High-res Image Gene #60: '10p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'10p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00512 (Fisher's exact test), Q value = 0.22

Table S13. Gene #60: '10p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	GLIOBLASTOMA MULTIFORME (GBM)	TREATED PRIMARY GBM	UNTREATED PRIMARY (DE NOVO) GBM
ALL	28	18	525
10P LOSS MUTATED	22	10	445
10P LOSS WILD-TYPE	6	8	80

Figure S13. Get High-res Image Gene #60: '10p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'10q loss' versus 'Time to Death'

P value = 0.000195 (logrank test), Q value = 0.012

Table S14. Gene #61: '10q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	570	470	0.1 - 127.6 (12.2)
10Q LOSS MUTATED	487	407	0.1 - 127.6 (11.9)
10Q LOSS WILD-TYPE	83	63	0.4 - 115.9 (14.5)

Figure S14. Get High-res Image Gene #61: '10q loss' versus Clinical Feature #1: 'Time to Death'

'10q loss' versus 'YEARS_TO_BIRTH'

P value = 1.32e-07 (Wilcoxon-test), Q value = 4.3e-05

Table S15. Gene #61: '10q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	571	57.7 (14.5)
10Q LOSS MUTATED	488	59.3 (13.0)
10Q LOSS WILD-TYPE	83	48.4 (18.6)

Figure S15. Get High-res Image Gene #61: '10q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

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/GBM-TP/19791352/transformed.cor.cli.txt
Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/GBM-TP/19775175/GBM-TP.merged_data.txt
Number of patients = 571
Number of significantly arm-level cnvs = 82
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.

Download Results

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

References

[1] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)

[2] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)

[3] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)

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