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

Brain Lower Grade Glioma (Primary solid tumor)

15 July 2014 | analyses__2014_07_15

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 (2014): Correlation between copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1RV0MFS

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 78 arm-level events and 8 clinical features across 400 patients, 27 significant findings detected with Q value < 0.25.

3q gain cnv correlated to 'Time to Death'.
7p gain cnv correlated to 'Time to Death' and 'AGE'.
7q gain cnv correlated to 'Time to Death' and 'AGE'.
19p gain cnv correlated to 'HISTOLOGICAL.TYPE'.
19q gain cnv correlated to 'Time to Death' and 'AGE'.
20p gain cnv correlated to 'Time to Death' and 'AGE'.
20q gain cnv correlated to 'Time to Death' and 'AGE'.
1p loss cnv correlated to 'HISTOLOGICAL.TYPE'.
6p loss cnv correlated to 'Time to Death'.
6q loss cnv correlated to 'Time to Death' and 'HISTOLOGICAL.TYPE'.
9p loss cnv correlated to 'Time to Death'.
10p loss cnv correlated to 'Time to Death', 'AGE', and 'HISTOLOGICAL.TYPE'.
10q loss cnv correlated to 'Time to Death', 'AGE', and 'HISTOLOGICAL.TYPE'.
14q loss cnv correlated to 'Time to Death'.
19q loss cnv correlated to 'HISTOLOGICAL.TYPE'.
22q loss cnv correlated to 'Time to Death' and 'AGE'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 78 arm-level events and 8 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 27 significant findings detected.


		Clinical Features	Time to Death	AGE	GENDER	KARNOFSKY PERFORMANCE SCORE	HISTOLOGICAL TYPE	RADIATIONS RADIATION REGIMENINDICATION	RACE	ETHNICITY
	nCNV (%)	nWild-Type	logrank test	Wilcoxon-test	Fisher's exact test	Wilcoxon-test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
10p loss	66 (16%)	334	0 (0)	1.09e-13 (6.72e-11)	0.498 (1.00)	0.00461 (1.00)	0.00016 (0.096)	0.423 (1.00)	0.015 (1.00)	1 (1.00)
10q loss	77 (19%)	323	6.06e-12 (3.74e-09)	3.12e-13 (1.93e-10)	0.445 (1.00)	0.0119 (1.00)	6e-05 (0.0362)	0.647 (1.00)	0.032 (1.00)	0.745 (1.00)
7p gain	92 (23%)	308	2.98e-05 (0.018)	1.29e-06 (0.000788)	0.122 (1.00)	0.151 (1.00)	0.182 (1.00)	0.67 (1.00)	0.0403 (1.00)	0.759 (1.00)
7q gain	121 (30%)	279	0.000128 (0.0771)	3.25e-07 (0.000199)	0.228 (1.00)	0.377 (1.00)	0.0738 (1.00)	0.794 (1.00)	0.0909 (1.00)	1 (1.00)
19q gain	20 (5%)	380	2.01e-05 (0.0122)	0.000236 (0.14)	0.819 (1.00)	0.201 (1.00)	0.153 (1.00)	0.784 (1.00)	0.127 (1.00)	0.55 (1.00)
20p gain	36 (9%)	364	7.9e-08 (4.86e-05)	2.13e-07 (0.000131)	0.484 (1.00)	0.0193 (1.00)	0.344 (1.00)	0.834 (1.00)	0.17 (1.00)	1 (1.00)
20q gain	37 (9%)	363	6.96e-08 (4.29e-05)	1.16e-06 (0.000712)	0.225 (1.00)	0.0388 (1.00)	0.437 (1.00)	0.684 (1.00)	0.275 (1.00)	1 (1.00)
6q loss	47 (12%)	353	0.000226 (0.135)	0.0382 (1.00)	1 (1.00)	0.0231 (1.00)	0.00013 (0.0781)	0.0954 (1.00)	0.085 (1.00)	0.68 (1.00)
22q loss	45 (11%)	355	0.0002 (0.119)	0.000221 (0.132)	0.526 (1.00)	0.031 (1.00)	0.251 (1.00)	0.85 (1.00)	0.172 (1.00)	1 (1.00)
3q gain	8 (2%)	392	0.000383 (0.228)	0.0349 (1.00)	0.308 (1.00)	0.269 (1.00)	0.063 (1.00)	0.384 (1.00)	1 (1.00)	1 (1.00)
19p gain	79 (20%)	321	0.528 (1.00)	0.00908 (1.00)	0.377 (1.00)	0.0978 (1.00)	1e-05 (0.0061)	0.763 (1.00)	0.494 (1.00)	0.509 (1.00)
1p loss	147 (37%)	253	0.00479 (1.00)	0.00202 (1.00)	0.835 (1.00)	0.694 (1.00)	1e-05 (0.0061)	0.0177 (1.00)	0.228 (1.00)	0.788 (1.00)
6p loss	24 (6%)	376	0.000177 (0.106)	0.142 (1.00)	0.836 (1.00)	0.446 (1.00)	0.0763 (1.00)	1 (1.00)	0.0924 (1.00)	0.587 (1.00)
9p loss	86 (22%)	314	2.65e-05 (0.016)	0.0552 (1.00)	0.391 (1.00)	0.377 (1.00)	0.0626 (1.00)	0.0277 (1.00)	0.603 (1.00)	0.746 (1.00)
14q loss	63 (16%)	337	1.5e-05 (0.00909)	0.000651 (0.386)	1 (1.00)	0.0429 (1.00)	0.175 (1.00)	0.409 (1.00)	0.111 (1.00)	0.485 (1.00)
19q loss	166 (42%)	234	0.0695 (1.00)	0.0224 (1.00)	0.919 (1.00)	0.748 (1.00)	1e-05 (0.0061)	0.179 (1.00)	1 (1.00)	0.79 (1.00)
1p gain	11 (3%)	389	0.00555 (1.00)	0.047 (1.00)	0.225 (1.00)	0.941 (1.00)	0.00449 (1.00)	0.714 (1.00)	1 (1.00)	1 (1.00)
1q gain	18 (4%)	382	0.424 (1.00)	0.000959 (0.566)	0.339 (1.00)	0.0892 (1.00)	0.163 (1.00)	0.565 (1.00)	1 (1.00)	1 (1.00)
2p gain	10 (2%)	390	0.703 (1.00)	0.208 (1.00)	0.754 (1.00)	0.21 (1.00)	0.52 (1.00)	1 (1.00)	1 (1.00)	0.311 (1.00)
2q gain	9 (2%)	391	0.77 (1.00)	0.44 (1.00)	0.515 (1.00)	0.21 (1.00)	0.438 (1.00)	1 (1.00)	1 (1.00)	0.282 (1.00)
3p gain	11 (3%)	389	0.00116 (0.681)	0.092 (1.00)	0.546 (1.00)	0.696 (1.00)	0.023 (1.00)	0.714 (1.00)	1 (1.00)	1 (1.00)
4p gain	9 (2%)	391	0.288 (1.00)	0.651 (1.00)	0.737 (1.00)	0.719 (1.00)	0.0717 (1.00)	0.69 (1.00)	0.332 (1.00)	1 (1.00)
4q gain	3 (1%)	397	0.662 (1.00)	0.393 (1.00)	1 (1.00)		0.628 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)
5p gain	8 (2%)	392	0.62 (1.00)	0.269 (1.00)	0.735 (1.00)	0.974 (1.00)	0.232 (1.00)	0.691 (1.00)	0.0723 (1.00)	1 (1.00)
5q gain	5 (1%)	395	0.453 (1.00)	0.614 (1.00)	0.658 (1.00)	0.96 (1.00)	0.644 (1.00)	0.591 (1.00)	0.0373 (1.00)	1 (1.00)
6p gain	7 (2%)	393	0.777 (1.00)	0.109 (1.00)	0.248 (1.00)	0.96 (1.00)	0.183 (1.00)	0.654 (1.00)	1 (1.00)	1 (1.00)
8p gain	37 (9%)	363	0.712 (1.00)	0.889 (1.00)	0.489 (1.00)	0.926 (1.00)	0.205 (1.00)	0.684 (1.00)	1 (1.00)	1 (1.00)
8q gain	44 (11%)	356	0.649 (1.00)	0.451 (1.00)	0.521 (1.00)	0.655 (1.00)	0.0181 (1.00)	1 (1.00)	0.753 (1.00)	1 (1.00)
9p gain	14 (4%)	386	0.0399 (1.00)	0.0141 (1.00)	0.0523 (1.00)	0.417 (1.00)	0.403 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)
9q gain	19 (5%)	381	0.0247 (1.00)	0.0122 (1.00)	0.00897 (1.00)	0.348 (1.00)	0.13 (1.00)	0.777 (1.00)	0.574 (1.00)	0.55 (1.00)
10p gain	38 (10%)	362	0.749 (1.00)	0.0609 (1.00)	0.231 (1.00)	0.215 (1.00)	0.0212 (1.00)	0.00152 (0.892)	1 (1.00)	0.0458 (1.00)
10q gain	7 (2%)	393	0.766 (1.00)	0.303 (1.00)	0.141 (1.00)	0.235 (1.00)	0.114 (1.00)	0.187 (1.00)	0.269 (1.00)	0.219 (1.00)
11p gain	27 (7%)	373	0.524 (1.00)	0.0225 (1.00)	0.232 (1.00)	0.827 (1.00)	0.0475 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)
11q gain	47 (12%)	353	0.548 (1.00)	0.0113 (1.00)	0.118 (1.00)	0.578 (1.00)	0.2 (1.00)	1 (1.00)	0.772 (1.00)	1 (1.00)
12p gain	27 (7%)	373	0.799 (1.00)	0.539 (1.00)	0.159 (1.00)	0.556 (1.00)	0.697 (1.00)	1 (1.00)	0.245 (1.00)	1 (1.00)
12q gain	13 (3%)	387	0.00165 (0.966)	0.2 (1.00)	0.403 (1.00)	0.202 (1.00)	1 (1.00)	0.741 (1.00)	0.103 (1.00)	1 (1.00)
13q gain	5 (1%)	395	0.493 (1.00)	0.814 (1.00)	1 (1.00)	0.0235 (1.00)	0.851 (1.00)	0.591 (1.00)	1 (1.00)	1 (1.00)
14q gain	3 (1%)	397	0.429 (1.00)	0.22 (1.00)	1 (1.00)		1 (1.00)	0.126 (1.00)	1 (1.00)	1 (1.00)
15q gain	8 (2%)	392	0.121 (1.00)	0.0102 (1.00)	0.475 (1.00)	0.27 (1.00)	0.234 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)
16p gain	14 (4%)	386	0.316 (1.00)	0.0308 (1.00)	0.413 (1.00)	0.434 (1.00)	0.291 (1.00)	0.523 (1.00)	0.442 (1.00)	1 (1.00)
16q gain	17 (4%)	383	0.178 (1.00)	0.683 (1.00)	0.465 (1.00)	0.906 (1.00)	0.029 (1.00)	0.55 (1.00)	0.514 (1.00)	1 (1.00)
17p gain	17 (4%)	383	0.0527 (1.00)	0.15 (1.00)	0.318 (1.00)	0.724 (1.00)	0.1 (1.00)	1 (1.00)	0.132 (1.00)	0.488 (1.00)
17q gain	19 (5%)	381	0.0102 (1.00)	0.346 (1.00)	0.346 (1.00)	0.916 (1.00)	0.176 (1.00)	1 (1.00)	0.142 (1.00)	0.488 (1.00)
18p gain	12 (3%)	388	0.0585 (1.00)	0.65 (1.00)	1 (1.00)	0.415 (1.00)	0.325 (1.00)	1 (1.00)	0.418 (1.00)	1 (1.00)
18q gain	9 (2%)	391	0.132 (1.00)	0.588 (1.00)	0.737 (1.00)	0.899 (1.00)	0.481 (1.00)	0.69 (1.00)	0.331 (1.00)	1 (1.00)
21q gain	21 (5%)	379	0.19 (1.00)	0.00774 (1.00)	0.501 (1.00)	0.182 (1.00)	0.815 (1.00)	0.792 (1.00)	0.18 (1.00)	1 (1.00)
22q gain	14 (4%)	386	0.883 (1.00)	0.0516 (1.00)	1 (1.00)	0.152 (1.00)	0.00947 (1.00)	1 (1.00)	1 (1.00)	0.367 (1.00)
xq gain	28 (7%)	372	0.91 (1.00)	0.539 (1.00)	0.00286 (1.00)	0.473 (1.00)	0.101 (1.00)	0.479 (1.00)	0.0931 (1.00)	0.311 (1.00)
1q loss	18 (4%)	382	0.961 (1.00)	0.047 (1.00)	0.339 (1.00)	0.234 (1.00)	0.114 (1.00)	0.251 (1.00)	0.0193 (1.00)	0.509 (1.00)
2p loss	14 (4%)	386	0.232 (1.00)	0.939 (1.00)	0.283 (1.00)	0.958 (1.00)	0.785 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)
2q loss	13 (3%)	387	0.884 (1.00)	0.136 (1.00)	0.403 (1.00)	0.417 (1.00)	0.109 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)
3p loss	19 (5%)	381	0.0248 (1.00)	0.952 (1.00)	0.346 (1.00)	0.00077 (0.456)	0.482 (1.00)	1 (1.00)	1 (1.00)	0.158 (1.00)
3q loss	23 (6%)	377	0.0227 (1.00)	0.482 (1.00)	0.0857 (1.00)	0.155 (1.00)	0.927 (1.00)	0.612 (1.00)	0.648 (1.00)	0.218 (1.00)
4p loss	56 (14%)	344	0.773 (1.00)	0.00233 (1.00)	0.112 (1.00)	0.634 (1.00)	0.00231 (1.00)	0.228 (1.00)	0.512 (1.00)	0.142 (1.00)
4q loss	72 (18%)	328	0.836 (1.00)	0.133 (1.00)	0.24 (1.00)	0.917 (1.00)	0.00539 (1.00)	0.351 (1.00)	0.714 (1.00)	0.0838 (1.00)
5p loss	28 (7%)	372	0.866 (1.00)	0.267 (1.00)	0.695 (1.00)	0.0929 (1.00)	0.0146 (1.00)	0.0158 (1.00)	0.691 (1.00)	0.614 (1.00)
5q loss	28 (7%)	372	0.0513 (1.00)	0.274 (1.00)	0.327 (1.00)	0.436 (1.00)	0.0522 (1.00)	0.0332 (1.00)	0.688 (1.00)	1 (1.00)
7p loss	3 (1%)	397	0.469 (1.00)	0.611 (1.00)	0.585 (1.00)		0.631 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)
7q loss	3 (1%)	397	0.634 (1.00)	0.906 (1.00)	1 (1.00)	0.899 (1.00)	0.627 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)
8p loss	13 (3%)	387	0.0366 (1.00)	0.177 (1.00)	0.781 (1.00)	0.135 (1.00)	0.164 (1.00)	0.497 (1.00)	0.107 (1.00)	0.418 (1.00)
8q loss	9 (2%)	391	0.00933 (1.00)	0.161 (1.00)	0.515 (1.00)	0.302 (1.00)	0.482 (1.00)	1 (1.00)	0.101 (1.00)	0.311 (1.00)
9q loss	34 (8%)	366	0.00806 (1.00)	0.177 (1.00)	0.857 (1.00)	0.015 (1.00)	1 (1.00)	0.831 (1.00)	0.194 (1.00)	0.632 (1.00)
11p loss	49 (12%)	351	0.424 (1.00)	0.376 (1.00)	0.357 (1.00)	0.114 (1.00)	0.0404 (1.00)	0.464 (1.00)	1 (1.00)	1 (1.00)
11q loss	17 (4%)	383	0.0132 (1.00)	0.102 (1.00)	0.808 (1.00)	0.0773 (1.00)	0.0527 (1.00)	0.382 (1.00)	1 (1.00)	0.509 (1.00)
12p loss	18 (4%)	382	0.856 (1.00)	0.237 (1.00)	0.634 (1.00)	0.802 (1.00)	0.199 (1.00)	0.565 (1.00)	1 (1.00)	1 (1.00)
12q loss	37 (9%)	363	0.476 (1.00)	0.208 (1.00)	0.863 (1.00)	0.576 (1.00)	0.0307 (1.00)	0.533 (1.00)	0.723 (1.00)	0.379 (1.00)
13q loss	94 (24%)	306	0.182 (1.00)	0.924 (1.00)	0.0962 (1.00)	0.405 (1.00)	0.558 (1.00)	0.0327 (1.00)	0.238 (1.00)	0.536 (1.00)
15q loss	36 (9%)	364	0.245 (1.00)	0.529 (1.00)	0.599 (1.00)	0.965 (1.00)	0.685 (1.00)	1 (1.00)	0.715 (1.00)	0.379 (1.00)
16p loss	10 (2%)	390	0.226 (1.00)	0.000879 (0.52)	0.523 (1.00)	0.242 (1.00)	0.718 (1.00)	1 (1.00)	1 (1.00)	0.339 (1.00)
16q loss	18 (4%)	382	0.148 (1.00)	0.00098 (0.577)	1 (1.00)	0.525 (1.00)	0.508 (1.00)	0.565 (1.00)	0.558 (1.00)	0.53 (1.00)
17p loss	12 (3%)	388	0.00697 (1.00)	0.0538 (1.00)	0.381 (1.00)	0.00296 (1.00)	0.615 (1.00)	0.478 (1.00)	1 (1.00)	0.0786 (1.00)
17q loss	8 (2%)	392	0.304 (1.00)	0.174 (1.00)	0.735 (1.00)	0.0326 (1.00)	0.824 (1.00)	0.691 (1.00)	1 (1.00)	0.0366 (1.00)
18p loss	58 (14%)	342	0.864 (1.00)	0.0188 (1.00)	0.0647 (1.00)	0.7 (1.00)	0.254 (1.00)	0.61 (1.00)	0.0914 (1.00)	0.448 (1.00)
18q loss	53 (13%)	347	0.659 (1.00)	0.046 (1.00)	0.374 (1.00)	0.979 (1.00)	0.162 (1.00)	0.861 (1.00)	0.103 (1.00)	0.428 (1.00)
19p loss	18 (4%)	382	0.269 (1.00)	0.827 (1.00)	0.634 (1.00)	0.342 (1.00)	0.954 (1.00)	0.0889 (1.00)	0.0227 (1.00)	0.488 (1.00)
20p loss	3 (1%)	397	0.49 (1.00)	0.449 (1.00)	0.585 (1.00)		1 (1.00)	0.531 (1.00)	1 (1.00)	1 (1.00)
21q loss	24 (6%)	376	0.672 (1.00)	0.758 (1.00)	0.672 (1.00)	0.00326 (1.00)	0.018 (1.00)	0.619 (1.00)	1 (1.00)	0.604 (1.00)
xq loss	53 (13%)	347	0.0159 (1.00)	0.326 (1.00)	0.374 (1.00)	0.507 (1.00)	0.834 (1.00)	1 (1.00)	0.496 (1.00)	1 (1.00)

'3q gain' versus 'Time to Death'

P value = 0.000383 (logrank test), Q value = 0.23

Table S1. Gene #6: '3q gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	395	71	0.0 - 211.2 (15.0)
3Q GAIN MUTATED	8	4	0.2 - 47.8 (9.1)
3Q GAIN WILD-TYPE	387	67	0.0 - 211.2 (15.0)

Figure S1. Get High-res Image Gene #6: '3q gain' versus Clinical Feature #1: 'Time to Death'

'7p gain' versus 'Time to Death'

P value = 2.98e-05 (logrank test), Q value = 0.018

Table S2. Gene #12: '7p gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	395	71	0.0 - 211.2 (15.0)
7P GAIN MUTATED	92	31	0.1 - 211.2 (14.0)
7P GAIN WILD-TYPE	303	40	0.0 - 182.3 (15.0)

Figure S2. Get High-res Image Gene #12: '7p gain' versus Clinical Feature #1: 'Time to Death'

'7p gain' versus 'AGE'

P value = 1.29e-06 (Wilcoxon-test), Q value = 0.00079

Table S3. Gene #12: '7p gain' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	400	43.2 (13.3)
7P GAIN MUTATED	92	49.2 (13.1)
7P GAIN WILD-TYPE	308	41.5 (12.9)

Figure S3. Get High-res Image Gene #12: '7p gain' versus Clinical Feature #2: 'AGE'

'7q gain' versus 'Time to Death'

P value = 0.000128 (logrank test), Q value = 0.077

Table S4. Gene #13: '7q gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	395	71	0.0 - 211.2 (15.0)
7Q GAIN MUTATED	119	36	0.1 - 211.2 (15.3)
7Q GAIN WILD-TYPE	276	35	0.0 - 182.3 (15.0)

Figure S4. Get High-res Image Gene #13: '7q gain' versus Clinical Feature #1: 'Time to Death'

'7q gain' versus 'AGE'

P value = 3.25e-07 (Wilcoxon-test), Q value = 2e-04

Table S5. Gene #13: '7q gain' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	400	43.2 (13.3)
7Q GAIN MUTATED	121	48.4 (13.2)
7Q GAIN WILD-TYPE	279	41.0 (12.8)

Figure S5. Get High-res Image Gene #13: '7q gain' versus Clinical Feature #2: 'AGE'

'19p gain' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0061

Table S6. Gene #33: '19p gain' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	143	104	153
19P GAIN MUTATED	14	16	49
19P GAIN WILD-TYPE	129	88	104

Figure S6. Get High-res Image Gene #33: '19p gain' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'19q gain' versus 'Time to Death'

P value = 2.01e-05 (logrank test), Q value = 0.012

Table S7. Gene #34: '19q gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	395	71	0.0 - 211.2 (15.0)
19Q GAIN MUTATED	20	7	0.5 - 49.5 (11.8)
19Q GAIN WILD-TYPE	375	64	0.0 - 211.2 (15.1)

Figure S7. Get High-res Image Gene #34: '19q gain' versus Clinical Feature #1: 'Time to Death'

'19q gain' versus 'AGE'

P value = 0.000236 (Wilcoxon-test), Q value = 0.14

Table S8. Gene #34: '19q gain' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	400	43.2 (13.3)
19Q GAIN MUTATED	20	54.4 (12.2)
19Q GAIN WILD-TYPE	380	42.7 (13.2)

Figure S8. Get High-res Image Gene #34: '19q gain' versus Clinical Feature #2: 'AGE'

'20p gain' versus 'Time to Death'

P value = 7.9e-08 (logrank test), Q value = 4.9e-05

Table S9. Gene #35: '20p gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	395	71	0.0 - 211.2 (15.0)
20P GAIN MUTATED	36	13	0.5 - 49.5 (12.2)
20P GAIN WILD-TYPE	359	58	0.0 - 211.2 (15.1)

Figure S9. Get High-res Image Gene #35: '20p gain' versus Clinical Feature #1: 'Time to Death'

'20p gain' versus 'AGE'

P value = 2.13e-07 (Wilcoxon-test), Q value = 0.00013

Table S10. Gene #35: '20p gain' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	400	43.2 (13.3)
20P GAIN MUTATED	36	54.9 (12.3)
20P GAIN WILD-TYPE	364	42.1 (12.9)

Figure S10. Get High-res Image Gene #35: '20p gain' versus Clinical Feature #2: 'AGE'

'20q gain' versus 'Time to Death'

P value = 6.96e-08 (logrank test), Q value = 4.3e-05

Table S11. Gene #36: '20q gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	395	71	0.0 - 211.2 (15.0)
20Q GAIN MUTATED	37	13	0.5 - 49.5 (12.2)
20Q GAIN WILD-TYPE	358	58	0.0 - 211.2 (15.1)

Figure S11. Get High-res Image Gene #36: '20q gain' versus Clinical Feature #1: 'Time to Death'

'20q gain' versus 'AGE'

P value = 1.16e-06 (Wilcoxon-test), Q value = 0.00071

Table S12. Gene #36: '20q gain' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	400	43.2 (13.3)
20Q GAIN MUTATED	37	54.1 (13.1)
20Q GAIN WILD-TYPE	363	42.1 (12.9)

Figure S12. Get High-res Image Gene #36: '20q gain' versus Clinical Feature #2: 'AGE'

'1p loss' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0061

Table S13. Gene #40: '1p loss' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	143	104	153
1P LOSS MUTATED	8	30	109
1P LOSS WILD-TYPE	135	74	44

Figure S13. Get High-res Image Gene #40: '1p loss' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'6p loss' versus 'Time to Death'

P value = 0.000177 (logrank test), Q value = 0.11

Table S14. Gene #50: '6p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	395	71	0.0 - 211.2 (15.0)
6P LOSS MUTATED	23	8	0.2 - 48.4 (15.7)
6P LOSS WILD-TYPE	372	63	0.0 - 211.2 (14.9)

Figure S14. Get High-res Image Gene #50: '6p loss' versus Clinical Feature #1: 'Time to Death'

'6q loss' versus 'Time to Death'

P value = 0.000226 (logrank test), Q value = 0.13

Table S15. Gene #51: '6q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	395	71	0.0 - 211.2 (15.0)
6Q LOSS MUTATED	45	12	0.1 - 57.9 (16.1)
6Q LOSS WILD-TYPE	350	59	0.0 - 211.2 (14.7)

Figure S15. Get High-res Image Gene #51: '6q loss' versus Clinical Feature #1: 'Time to Death'

'6q loss' versus 'HISTOLOGICAL.TYPE'

P value = 0.00013 (Fisher's exact test), Q value = 0.078

Table S16. Gene #51: '6q loss' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	143	104	153
6Q LOSS MUTATED	30	9	8
6Q LOSS WILD-TYPE	113	95	145

Figure S16. Get High-res Image Gene #51: '6q loss' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'9p loss' versus 'Time to Death'

P value = 2.65e-05 (logrank test), Q value = 0.016

Table S17. Gene #56: '9p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	395	71	0.0 - 211.2 (15.0)
9P LOSS MUTATED	85	26	0.1 - 117.4 (15.0)
9P LOSS WILD-TYPE	310	45	0.0 - 211.2 (15.0)

Figure S17. Get High-res Image Gene #56: '9p loss' versus Clinical Feature #1: 'Time to Death'

'10p loss' versus 'Time to Death'

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

Table S18. Gene #58: '10p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	395	71	0.0 - 211.2 (15.0)
10P LOSS MUTATED	66	30	0.1 - 134.3 (11.8)
10P LOSS WILD-TYPE	329	41	0.0 - 211.2 (15.3)

Figure S18. Get High-res Image Gene #58: '10p loss' versus Clinical Feature #1: 'Time to Death'

'10p loss' versus 'AGE'

P value = 1.09e-13 (Wilcoxon-test), Q value = 6.7e-11

Table S19. Gene #58: '10p loss' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	400	43.2 (13.3)
10P LOSS MUTATED	66	54.6 (11.5)
10P LOSS WILD-TYPE	334	41.0 (12.5)

Figure S19. Get High-res Image Gene #58: '10p loss' versus Clinical Feature #2: 'AGE'

'10p loss' versus 'HISTOLOGICAL.TYPE'

P value = 0.00016 (Fisher's exact test), Q value = 0.096

Table S20. Gene #58: '10p loss' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	143	104	153
10P LOSS MUTATED	39	13	14
10P LOSS WILD-TYPE	104	91	139

Figure S20. Get High-res Image Gene #58: '10p loss' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'10q loss' versus 'Time to Death'

P value = 6.06e-12 (logrank test), Q value = 3.7e-09

Table S21. Gene #59: '10q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	395	71	0.0 - 211.2 (15.0)
10Q LOSS MUTATED	76	34	0.1 - 156.2 (12.3)
10Q LOSS WILD-TYPE	319	37	0.0 - 211.2 (15.2)

Figure S21. Get High-res Image Gene #59: '10q loss' versus Clinical Feature #1: 'Time to Death'

'10q loss' versus 'AGE'

P value = 3.12e-13 (Wilcoxon-test), Q value = 1.9e-10

Table S22. Gene #59: '10q loss' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	400	43.2 (13.3)
10Q LOSS MUTATED	77	53.3 (12.5)
10Q LOSS WILD-TYPE	323	40.9 (12.4)

Figure S22. Get High-res Image Gene #59: '10q loss' versus Clinical Feature #2: 'AGE'

'10q loss' versus 'HISTOLOGICAL.TYPE'

P value = 6e-05 (Fisher's exact test), Q value = 0.036

Table S23. Gene #59: '10q loss' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	143	104	153
10Q LOSS MUTATED	45	15	17
10Q LOSS WILD-TYPE	98	89	136

Figure S23. Get High-res Image Gene #59: '10q loss' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'14q loss' versus 'Time to Death'

P value = 1.5e-05 (logrank test), Q value = 0.0091

Table S24. Gene #65: '14q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	395	71	0.0 - 211.2 (15.0)
14Q LOSS MUTATED	61	21	0.1 - 130.8 (15.0)
14Q LOSS WILD-TYPE	334	50	0.0 - 211.2 (15.0)

Figure S24. Get High-res Image Gene #65: '14q loss' versus Clinical Feature #1: 'Time to Death'

'19q loss' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0061

Table S25. Gene #74: '19q loss' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	143	104	153
19Q LOSS MUTATED	17	33	116
19Q LOSS WILD-TYPE	126	71	37

Figure S25. Get High-res Image Gene #74: '19q loss' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'22q loss' versus 'Time to Death'

P value = 2e-04 (logrank test), Q value = 0.12

Table S26. Gene #77: '22q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	395	71	0.0 - 211.2 (15.0)
22Q LOSS MUTATED	45	17	0.1 - 156.2 (15.5)
22Q LOSS WILD-TYPE	350	54	0.0 - 211.2 (15.0)

Figure S26. Get High-res Image Gene #77: '22q loss' versus Clinical Feature #1: 'Time to Death'

'22q loss' versus 'AGE'

P value = 0.000221 (Wilcoxon-test), Q value = 0.13

Table S27. Gene #77: '22q loss' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	400	43.2 (13.3)
22Q LOSS MUTATED	45	50.6 (13.7)
22Q LOSS WILD-TYPE	355	42.3 (13.0)

Figure S27. Get High-res Image Gene #77: '22q loss' versus Clinical Feature #2: 'AGE'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Clinical data file = LGG-TP.merged_data.txt
Number of patients = 400
Number of significantly arm-level cnvs = 78
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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