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

Brain Lower Grade Glioma (Primary solid tumor)

17 October 2014 | analyses__2014_10_17

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/C1NC603C

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 430 patients, 28 significant findings detected with Q value < 0.25.

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'.
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' and 'AGE'.
16p loss cnv correlated to 'AGE'.
16q loss cnv correlated to 'AGE'.
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, 28 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	68 (16%)	362	0 (0)	3.81e-15 (2.36e-12)	0.506 (1.00)	0.00292 (1.00)	6e-05 (0.0359)	0.625 (1.00)	0.0277 (1.00)	1 (1.00)
10q loss	80 (19%)	350	4.77e-15 (2.95e-12)	1.37e-13 (8.42e-11)	0.384 (1.00)	0.0147 (1.00)	3e-05 (0.018)	0.76 (1.00)	0.0701 (1.00)	0.747 (1.00)
7p gain	96 (22%)	334	9.61e-06 (0.00583)	1.07e-06 (0.000651)	0.201 (1.00)	0.179 (1.00)	0.0965 (1.00)	0.568 (1.00)	0.0703 (1.00)	0.767 (1.00)
7q gain	127 (30%)	303	2.27e-05 (0.0137)	2.84e-07 (0.000174)	0.456 (1.00)	0.452 (1.00)	0.0223 (1.00)	0.696 (1.00)	0.128 (1.00)	1 (1.00)
19q gain	20 (5%)	410	2.76e-06 (0.00168)	0.000164 (0.098)	0.819 (1.00)	0.229 (1.00)	0.139 (1.00)	0.579 (1.00)	0.199 (1.00)	0.545 (1.00)
20p gain	37 (9%)	393	8.06e-08 (4.96e-05)	5.41e-07 (0.000332)	0.606 (1.00)	0.0301 (1.00)	0.319 (1.00)	1 (1.00)	0.326 (1.00)	1 (1.00)
20q gain	37 (9%)	393	1.27e-08 (7.8e-06)	7.13e-07 (0.000436)	0.228 (1.00)	0.0534 (1.00)	0.523 (1.00)	1 (1.00)	0.527 (1.00)	1 (1.00)
6q loss	50 (12%)	380	4.27e-06 (0.0026)	0.051 (1.00)	0.65 (1.00)	0.0061 (1.00)	0.0003 (0.178)	0.0951 (1.00)	0.0886 (1.00)	0.696 (1.00)
14q loss	65 (15%)	365	4.3e-06 (0.00261)	0.000162 (0.0965)	0.893 (1.00)	0.0442 (1.00)	0.183 (1.00)	0.507 (1.00)	0.252 (1.00)	0.486 (1.00)
22q loss	46 (11%)	384	2.92e-05 (0.0175)	5.45e-05 (0.0326)	0.639 (1.00)	0.0245 (1.00)	0.228 (1.00)	1 (1.00)	0.169 (1.00)	1 (1.00)
19p gain	84 (20%)	346	0.684 (1.00)	0.0113 (1.00)	0.465 (1.00)	0.109 (1.00)	1e-05 (0.00606)	0.765 (1.00)	0.567 (1.00)	0.53 (1.00)
1p loss	159 (37%)	271	0.00125 (0.734)	0.000641 (0.378)	1 (1.00)	0.768 (1.00)	1e-05 (0.00606)	0.0188 (1.00)	0.351 (1.00)	1 (1.00)
6p loss	25 (6%)	405	1.26e-05 (0.00757)	0.156 (1.00)	1 (1.00)	0.298 (1.00)	0.153 (1.00)	1 (1.00)	0.116 (1.00)	0.6 (1.00)
16p loss	11 (3%)	419	0.0632 (1.00)	0.000198 (0.118)	0.36 (1.00)	0.155 (1.00)	0.544 (1.00)	1 (1.00)	1 (1.00)	0.363 (1.00)
16q loss	19 (4%)	411	0.0525 (1.00)	0.000259 (0.154)	1 (1.00)	0.384 (1.00)	0.362 (1.00)	0.563 (1.00)	0.629 (1.00)	0.545 (1.00)
19q loss	177 (41%)	253	0.0265 (1.00)	0.0109 (1.00)	1 (1.00)	0.543 (1.00)	1e-05 (0.00606)	0.185 (1.00)	0.924 (1.00)	0.801 (1.00)
1p gain	11 (3%)	419	0.00637 (1.00)	0.0415 (1.00)	0.227 (1.00)	0.988 (1.00)	0.00666 (1.00)	0.704 (1.00)	1 (1.00)	1 (1.00)
1q gain	18 (4%)	412	0.38 (1.00)	0.000736 (0.433)	0.342 (1.00)	0.108 (1.00)	0.204 (1.00)	0.55 (1.00)	1 (1.00)	1 (1.00)
2p gain	11 (3%)	419	0.944 (1.00)	0.103 (1.00)	0.548 (1.00)	0.261 (1.00)	0.502 (1.00)	1 (1.00)	1 (1.00)	0.336 (1.00)
2q gain	10 (2%)	420	0.58 (1.00)	0.237 (1.00)	0.348 (1.00)	0.261 (1.00)	0.609 (1.00)	1 (1.00)	1 (1.00)	0.308 (1.00)
3p gain	11 (3%)	419	0.00159 (0.931)	0.0819 (1.00)	0.548 (1.00)	0.748 (1.00)	0.0243 (1.00)	0.704 (1.00)	1 (1.00)	1 (1.00)
3q gain	8 (2%)	422	0.000563 (0.333)	0.0314 (1.00)	0.31 (1.00)	0.292 (1.00)	0.0786 (1.00)	0.371 (1.00)	1 (1.00)	1 (1.00)
4p gain	11 (3%)	419	0.269 (1.00)	0.849 (1.00)	1 (1.00)	0.986 (1.00)	0.0236 (1.00)	0.473 (1.00)	0.434 (1.00)	1 (1.00)
4q gain	4 (1%)	426	0.604 (1.00)	0.737 (1.00)	1 (1.00)		0.377 (1.00)	0.585 (1.00)	1 (1.00)	1 (1.00)
5p gain	8 (2%)	422	0.634 (1.00)	0.242 (1.00)	0.736 (1.00)	0.911 (1.00)	0.233 (1.00)	1 (1.00)	0.128 (1.00)	1 (1.00)
5q gain	5 (1%)	425	0.431 (1.00)	0.582 (1.00)	0.659 (1.00)	0.993 (1.00)	0.648 (1.00)	0.588 (1.00)	0.0703 (1.00)	1 (1.00)
6p gain	7 (2%)	423	0.809 (1.00)	0.12 (1.00)	0.249 (1.00)	0.993 (1.00)	0.205 (1.00)	0.638 (1.00)	1 (1.00)	1 (1.00)
8p gain	39 (9%)	391	0.725 (1.00)	0.944 (1.00)	0.502 (1.00)	0.976 (1.00)	0.127 (1.00)	0.836 (1.00)	1 (1.00)	1 (1.00)
8q gain	46 (11%)	384	0.657 (1.00)	0.353 (1.00)	0.531 (1.00)	0.563 (1.00)	0.0102 (1.00)	0.848 (1.00)	0.841 (1.00)	1 (1.00)
9p gain	14 (3%)	416	0.0704 (1.00)	0.0117 (1.00)	0.0531 (1.00)	0.47 (1.00)	0.424 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)
9q gain	20 (5%)	410	0.0652 (1.00)	0.0149 (1.00)	0.0053 (1.00)	0.403 (1.00)	0.105 (1.00)	0.777 (1.00)	0.197 (1.00)	0.564 (1.00)
10p gain	44 (10%)	386	0.798 (1.00)	0.0616 (1.00)	0.2 (1.00)	0.182 (1.00)	0.0117 (1.00)	0.00496 (1.00)	0.714 (1.00)	0.0734 (1.00)
10q gain	8 (2%)	422	0.78 (1.00)	0.29 (1.00)	0.475 (1.00)	0.221 (1.00)	0.0787 (1.00)	0.371 (1.00)	0.0475 (1.00)	0.249 (1.00)
11p gain	27 (6%)	403	0.492 (1.00)	0.0181 (1.00)	0.235 (1.00)	0.747 (1.00)	0.0353 (1.00)	0.808 (1.00)	0.748 (1.00)	1 (1.00)
11q gain	49 (11%)	381	0.515 (1.00)	0.0188 (1.00)	0.126 (1.00)	0.681 (1.00)	0.36 (1.00)	1 (1.00)	0.854 (1.00)	1 (1.00)
12p gain	27 (6%)	403	0.751 (1.00)	0.594 (1.00)	0.16 (1.00)	0.618 (1.00)	0.587 (1.00)	0.808 (1.00)	0.305 (1.00)	1 (1.00)
12q gain	13 (3%)	417	0.00182 (1.00)	0.186 (1.00)	0.403 (1.00)	0.221 (1.00)	1 (1.00)	1 (1.00)	0.251 (1.00)	1 (1.00)
13q gain	6 (1%)	424	0.459 (1.00)	0.925 (1.00)	1 (1.00)	0.041 (1.00)	0.885 (1.00)	0.353 (1.00)	1 (1.00)	1 (1.00)
14q gain	3 (1%)	427	0.404 (1.00)	0.203 (1.00)	1 (1.00)		1 (1.00)	0.11 (1.00)	1 (1.00)	1 (1.00)
15q gain	8 (2%)	422	0.0939 (1.00)	0.00867 (1.00)	0.475 (1.00)	0.293 (1.00)	0.231 (1.00)	0.672 (1.00)	1 (1.00)	1 (1.00)
16p gain	16 (4%)	414	0.377 (1.00)	0.112 (1.00)	0.443 (1.00)	0.518 (1.00)	0.113 (1.00)	0.752 (1.00)	0.542 (1.00)	1 (1.00)
16q gain	18 (4%)	412	0.162 (1.00)	0.785 (1.00)	0.342 (1.00)	0.856 (1.00)	0.0226 (1.00)	0.55 (1.00)	0.59 (1.00)	1 (1.00)
17p gain	17 (4%)	413	0.0691 (1.00)	0.125 (1.00)	0.319 (1.00)	0.645 (1.00)	0.129 (1.00)	0.762 (1.00)	0.314 (1.00)	0.484 (1.00)
17q gain	19 (4%)	411	0.0149 (1.00)	0.305 (1.00)	0.346 (1.00)	1 (1.00)	0.248 (1.00)	1 (1.00)	0.332 (1.00)	0.484 (1.00)
18p gain	13 (3%)	417	0.0585 (1.00)	0.86 (1.00)	0.781 (1.00)	0.454 (1.00)	0.248 (1.00)	1 (1.00)	0.49 (1.00)	1 (1.00)
18q gain	9 (2%)	421	0.121 (1.00)	0.535 (1.00)	0.737 (1.00)	0.947 (1.00)	0.432 (1.00)	0.692 (1.00)	0.372 (1.00)	1 (1.00)
21q gain	21 (5%)	409	0.177 (1.00)	0.00625 (1.00)	0.502 (1.00)	0.212 (1.00)	0.814 (1.00)	0.782 (1.00)	0.409 (1.00)	1 (1.00)
22q gain	15 (3%)	415	0.79 (1.00)	0.0435 (1.00)	0.797 (1.00)	0.173 (1.00)	0.0243 (1.00)	1 (1.00)	1 (1.00)	0.389 (1.00)
xq gain	30 (7%)	400	0.922 (1.00)	0.465 (1.00)	0.00389 (1.00)	0.404 (1.00)	0.0733 (1.00)	0.482 (1.00)	0.23 (1.00)	0.108 (1.00)
1q loss	23 (5%)	407	0.732 (1.00)	0.0469 (1.00)	0.83 (1.00)	0.959 (1.00)	0.0287 (1.00)	0.595 (1.00)	0.143 (1.00)	0.6 (1.00)
2p loss	16 (4%)	414	0.263 (1.00)	0.845 (1.00)	0.318 (1.00)	0.784 (1.00)	0.477 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)
2q loss	13 (3%)	417	0.909 (1.00)	0.156 (1.00)	0.403 (1.00)	0.47 (1.00)	0.127 (1.00)	0.737 (1.00)	1 (1.00)	1 (1.00)
3p loss	21 (5%)	409	0.0533 (1.00)	0.66 (1.00)	0.178 (1.00)	0.000528 (0.313)	0.608 (1.00)	1 (1.00)	1 (1.00)	0.185 (1.00)
3q loss	23 (5%)	407	0.0166 (1.00)	0.427 (1.00)	0.0856 (1.00)	0.186 (1.00)	0.963 (1.00)	0.595 (1.00)	0.705 (1.00)	0.215 (1.00)
4p loss	58 (13%)	372	0.753 (1.00)	0.00391 (1.00)	0.0654 (1.00)	0.734 (1.00)	0.00201 (1.00)	0.166 (1.00)	0.422 (1.00)	0.143 (1.00)
4q loss	74 (17%)	356	0.782 (1.00)	0.155 (1.00)	0.158 (1.00)	0.942 (1.00)	0.0051 (1.00)	0.27 (1.00)	0.751 (1.00)	0.0868 (1.00)
5p loss	28 (7%)	402	0.89 (1.00)	0.224 (1.00)	0.695 (1.00)	0.115 (1.00)	0.0148 (1.00)	0.00622 (1.00)	0.761 (1.00)	0.614 (1.00)
5q loss	28 (7%)	402	0.054 (1.00)	0.229 (1.00)	0.329 (1.00)	0.515 (1.00)	0.0669 (1.00)	0.0264 (1.00)	0.762 (1.00)	1 (1.00)
7p loss	3 (1%)	427	0.546 (1.00)	0.64 (1.00)	0.586 (1.00)		0.628 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)
7q loss	3 (1%)	427	0.677 (1.00)	0.94 (1.00)	1 (1.00)	0.925 (1.00)	0.627 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)
8p loss	13 (3%)	417	0.0589 (1.00)	0.152 (1.00)	0.781 (1.00)	0.157 (1.00)	0.248 (1.00)	0.319 (1.00)	0.253 (1.00)	0.414 (1.00)
8q loss	9 (2%)	421	0.0211 (1.00)	0.14 (1.00)	0.517 (1.00)	0.339 (1.00)	0.434 (1.00)	1 (1.00)	0.17 (1.00)	0.308 (1.00)
9p loss	96 (22%)	334	0.000583 (0.344)	0.0636 (1.00)	0.816 (1.00)	0.237 (1.00)	0.083 (1.00)	0.0461 (1.00)	0.745 (1.00)	0.539 (1.00)
9q loss	38 (9%)	392	0.0629 (1.00)	0.189 (1.00)	0.865 (1.00)	0.014 (1.00)	0.952 (1.00)	1 (1.00)	0.16 (1.00)	0.645 (1.00)
11p loss	53 (12%)	377	0.285 (1.00)	0.464 (1.00)	0.463 (1.00)	0.122 (1.00)	0.011 (1.00)	0.471 (1.00)	1 (1.00)	1 (1.00)
11q loss	19 (4%)	411	0.00335 (1.00)	0.0684 (1.00)	0.816 (1.00)	0.0654 (1.00)	0.0216 (1.00)	0.388 (1.00)	1 (1.00)	0.545 (1.00)
12p loss	21 (5%)	409	0.774 (1.00)	0.342 (1.00)	0.502 (1.00)	0.398 (1.00)	0.162 (1.00)	0.782 (1.00)	1 (1.00)	1 (1.00)
12q loss	40 (9%)	390	0.436 (1.00)	0.295 (1.00)	0.739 (1.00)	0.334 (1.00)	0.0344 (1.00)	0.538 (1.00)	0.686 (1.00)	0.382 (1.00)
13q loss	98 (23%)	332	0.156 (1.00)	0.672 (1.00)	0.105 (1.00)	0.26 (1.00)	0.534 (1.00)	0.0161 (1.00)	0.441 (1.00)	0.382 (1.00)
15q loss	39 (9%)	391	0.173 (1.00)	0.671 (1.00)	0.502 (1.00)	0.952 (1.00)	0.77 (1.00)	1 (1.00)	0.804 (1.00)	1 (1.00)
17p loss	12 (3%)	418	0.0148 (1.00)	0.0464 (1.00)	0.383 (1.00)	0.00305 (1.00)	0.706 (1.00)	0.473 (1.00)	1 (1.00)	0.0774 (1.00)
17q loss	8 (2%)	422	0.44 (1.00)	0.155 (1.00)	0.736 (1.00)	0.0341 (1.00)	0.825 (1.00)	1 (1.00)	1 (1.00)	0.036 (1.00)
18p loss	59 (14%)	371	0.664 (1.00)	0.00674 (1.00)	0.0491 (1.00)	0.681 (1.00)	0.313 (1.00)	0.733 (1.00)	0.0727 (1.00)	0.453 (1.00)
18q loss	54 (13%)	376	0.666 (1.00)	0.0524 (1.00)	0.306 (1.00)	0.899 (1.00)	0.203 (1.00)	1 (1.00)	0.0995 (1.00)	0.433 (1.00)
19p loss	19 (4%)	411	0.358 (1.00)	0.971 (1.00)	0.816 (1.00)	0.174 (1.00)	0.956 (1.00)	0.0853 (1.00)	0.11 (1.00)	0.505 (1.00)
20p loss	5 (1%)	425	0.657 (1.00)	0.99 (1.00)	0.659 (1.00)		0.547 (1.00)	1 (1.00)	0.0903 (1.00)	1 (1.00)
21q loss	26 (6%)	404	0.686 (1.00)	0.859 (1.00)	0.317 (1.00)	0.00207 (1.00)	0.0262 (1.00)	0.622 (1.00)	1 (1.00)	1 (1.00)
xq loss	56 (13%)	374	0.0239 (1.00)	0.201 (1.00)	0.195 (1.00)	0.478 (1.00)	0.887 (1.00)	0.861 (1.00)	0.401 (1.00)	1 (1.00)

'7p gain' versus 'Time to Death'

P value = 9.61e-06 (logrank test), Q value = 0.0058

Table S1. Gene #12: '7p gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	427	75	0.0 - 211.2 (15.9)
7P GAIN MUTATED	96	32	0.1 - 211.2 (14.9)
7P GAIN WILD-TYPE	331	43	0.0 - 182.3 (16.0)

Figure S1. Get High-res Image Gene #12: '7p gain' versus Clinical Feature #1: 'Time to Death'

'7p gain' versus 'AGE'

P value = 1.07e-06 (Wilcoxon-test), Q value = 0.00065

Table S2. Gene #12: '7p gain' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	429	43.0 (13.2)
7P GAIN MUTATED	96	48.9 (13.1)
7P GAIN WILD-TYPE	333	41.3 (12.8)

Figure S2. Get High-res Image Gene #12: '7p gain' versus Clinical Feature #2: 'AGE'

'7q gain' versus 'Time to Death'

P value = 2.27e-05 (logrank test), Q value = 0.014

Table S3. Gene #13: '7q gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	427	75	0.0 - 211.2 (15.9)
7Q GAIN MUTATED	127	38	0.1 - 211.2 (15.3)
7Q GAIN WILD-TYPE	300	37	0.0 - 182.3 (16.1)

Figure S3. Get High-res Image Gene #13: '7q gain' versus Clinical Feature #1: 'Time to Death'

'7q gain' versus 'AGE'

P value = 2.84e-07 (Wilcoxon-test), Q value = 0.00017

Table S4. Gene #13: '7q gain' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	429	43.0 (13.2)
7Q GAIN MUTATED	127	48.1 (13.2)
7Q GAIN WILD-TYPE	302	40.8 (12.7)

Figure S4. 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 S5. Gene #33: '19p gain' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	159	107	164
19P GAIN MUTATED	16	16	52
19P GAIN WILD-TYPE	143	91	112

Figure S5. Get High-res Image Gene #33: '19p gain' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'19q gain' versus 'Time to Death'

P value = 2.76e-06 (logrank test), Q value = 0.0017

Table S6. Gene #34: '19q gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	427	75	0.0 - 211.2 (15.9)
19Q GAIN MUTATED	20	8	0.5 - 49.5 (14.1)
19Q GAIN WILD-TYPE	407	67	0.0 - 211.2 (16.0)

Figure S6. Get High-res Image Gene #34: '19q gain' versus Clinical Feature #1: 'Time to Death'

'19q gain' versus 'AGE'

P value = 0.000164 (Wilcoxon-test), Q value = 0.098

Table S7. Gene #34: '19q gain' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	429	43.0 (13.2)
19Q GAIN MUTATED	20	54.4 (12.2)
19Q GAIN WILD-TYPE	409	42.4 (13.1)

Figure S7. Get High-res Image Gene #34: '19q gain' versus Clinical Feature #2: 'AGE'

'20p gain' versus 'Time to Death'

P value = 8.06e-08 (logrank test), Q value = 5e-05

Table S8. Gene #35: '20p gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	427	75	0.0 - 211.2 (15.9)
20P GAIN MUTATED	37	14	0.5 - 49.5 (13.5)
20P GAIN WILD-TYPE	390	61	0.0 - 211.2 (16.1)

Figure S8. Get High-res Image Gene #35: '20p gain' versus Clinical Feature #1: 'Time to Death'

'20p gain' versus 'AGE'

P value = 5.41e-07 (Wilcoxon-test), Q value = 0.00033

Table S9. Gene #35: '20p gain' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	429	43.0 (13.2)
20P GAIN MUTATED	37	54.2 (12.9)
20P GAIN WILD-TYPE	392	41.9 (12.8)

Figure S9. Get High-res Image Gene #35: '20p gain' versus Clinical Feature #2: 'AGE'

'20q gain' versus 'Time to Death'

P value = 1.27e-08 (logrank test), Q value = 7.8e-06

Table S10. Gene #36: '20q gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	427	75	0.0 - 211.2 (15.9)
20Q GAIN MUTATED	37	14	0.5 - 49.5 (13.5)
20Q GAIN WILD-TYPE	390	61	0.0 - 211.2 (16.1)

Figure S10. Get High-res Image Gene #36: '20q gain' versus Clinical Feature #1: 'Time to Death'

'20q gain' versus 'AGE'

P value = 7.13e-07 (Wilcoxon-test), Q value = 0.00044

Table S11. Gene #36: '20q gain' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	429	43.0 (13.2)
20Q GAIN MUTATED	37	54.1 (13.1)
20Q GAIN WILD-TYPE	392	41.9 (12.8)

Figure S11. 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 S12. Gene #40: '1p loss' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	159	107	164
1P LOSS MUTATED	9	32	118
1P LOSS WILD-TYPE	150	75	46

Figure S12. Get High-res Image Gene #40: '1p loss' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'6p loss' versus 'Time to Death'

P value = 1.26e-05 (logrank test), Q value = 0.0076

Table S13. Gene #50: '6p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	427	75	0.0 - 211.2 (15.9)
6P LOSS MUTATED	25	9	0.2 - 48.4 (15.5)
6P LOSS WILD-TYPE	402	66	0.0 - 211.2 (16.0)

Figure S13. Get High-res Image Gene #50: '6p loss' versus Clinical Feature #1: 'Time to Death'

'6q loss' versus 'Time to Death'

P value = 4.27e-06 (logrank test), Q value = 0.0026

Table S14. Gene #51: '6q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	427	75	0.0 - 211.2 (15.9)
6Q LOSS MUTATED	49	14	0.1 - 57.9 (15.5)
6Q LOSS WILD-TYPE	378	61	0.0 - 211.2 (16.0)

Figure S14. Get High-res Image Gene #51: '6q loss' versus Clinical Feature #1: 'Time to Death'

'6q loss' versus 'HISTOLOGICAL.TYPE'

P value = 3e-04 (Fisher's exact test), Q value = 0.18

Table S15. Gene #51: '6q loss' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	159	107	164
6Q LOSS MUTATED	31	10	9
6Q LOSS WILD-TYPE	128	97	155

Figure S15. Get High-res Image Gene #51: '6q loss' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'10p loss' versus 'Time to Death'

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

Table S16. Gene #58: '10p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	427	75	0.0 - 211.2 (15.9)
10P LOSS MUTATED	68	32	0.1 - 134.3 (12.2)
10P LOSS WILD-TYPE	359	43	0.0 - 211.2 (16.4)

Figure S16. Get High-res Image Gene #58: '10p loss' versus Clinical Feature #1: 'Time to Death'

'10p loss' versus 'AGE'

P value = 3.81e-15 (Wilcoxon-test), Q value = 2.4e-12

Table S17. Gene #58: '10p loss' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	429	43.0 (13.2)
10P LOSS MUTATED	68	55.0 (11.5)
10P LOSS WILD-TYPE	361	40.7 (12.3)

Figure S17. Get High-res Image Gene #58: '10p loss' versus Clinical Feature #2: 'AGE'

'10p loss' versus 'HISTOLOGICAL.TYPE'

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

Table S18. Gene #58: '10p loss' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	159	107	164
10P LOSS MUTATED	41	13	14
10P LOSS WILD-TYPE	118	94	150

Figure S18. Get High-res Image Gene #58: '10p loss' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'10q loss' versus 'Time to Death'

P value = 4.77e-15 (logrank test), Q value = 3e-12

Table S19. Gene #59: '10q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	427	75	0.0 - 211.2 (15.9)
10Q LOSS MUTATED	80	37	0.1 - 156.2 (13.0)
10Q LOSS WILD-TYPE	347	38	0.0 - 211.2 (16.5)

Figure S19. Get High-res Image Gene #59: '10q loss' versus Clinical Feature #1: 'Time to Death'

'10q loss' versus 'AGE'

P value = 1.37e-13 (Wilcoxon-test), Q value = 8.4e-11

Table S20. Gene #59: '10q loss' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	429	43.0 (13.2)
10Q LOSS MUTATED	80	53.0 (12.5)
10Q LOSS WILD-TYPE	349	40.7 (12.3)

Figure S20. Get High-res Image Gene #59: '10q loss' versus Clinical Feature #2: 'AGE'

'10q loss' versus 'HISTOLOGICAL.TYPE'

P value = 3e-05 (Fisher's exact test), Q value = 0.018

Table S21. Gene #59: '10q loss' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	159	107	164
10Q LOSS MUTATED	48	15	17
10Q LOSS WILD-TYPE	111	92	147

Figure S21. Get High-res Image Gene #59: '10q loss' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'14q loss' versus 'Time to Death'

P value = 4.3e-06 (logrank test), Q value = 0.0026

Table S22. Gene #65: '14q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	427	75	0.0 - 211.2 (15.9)
14Q LOSS MUTATED	63	22	0.1 - 130.8 (15.5)
14Q LOSS WILD-TYPE	364	53	0.0 - 211.2 (16.0)

Figure S22. Get High-res Image Gene #65: '14q loss' versus Clinical Feature #1: 'Time to Death'

'14q loss' versus 'AGE'

P value = 0.000162 (Wilcoxon-test), Q value = 0.096

Table S23. Gene #65: '14q loss' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	429	43.0 (13.2)
14Q LOSS MUTATED	65	48.8 (13.0)
14Q LOSS WILD-TYPE	364	41.9 (13.0)

Figure S23. Get High-res Image Gene #65: '14q loss' versus Clinical Feature #2: 'AGE'

'16p loss' versus 'AGE'

P value = 0.000198 (Wilcoxon-test), Q value = 0.12

Table S24. Gene #67: '16p loss' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	429	43.0 (13.2)
16P LOSS MUTATED	11	58.5 (10.3)
16P LOSS WILD-TYPE	418	42.6 (13.1)

Figure S24. Get High-res Image Gene #67: '16p loss' versus Clinical Feature #2: 'AGE'

'16q loss' versus 'AGE'

P value = 0.000259 (Wilcoxon-test), Q value = 0.15

Table S25. Gene #68: '16q loss' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	429	43.0 (13.2)
16Q LOSS MUTATED	19	55.3 (14.3)
16Q LOSS WILD-TYPE	410	42.4 (12.9)

Figure S25. Get High-res Image Gene #68: '16q loss' versus Clinical Feature #2: 'AGE'

'19q loss' versus 'HISTOLOGICAL.TYPE'

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

Table S26. Gene #74: '19q loss' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	159	107	164
19Q LOSS MUTATED	18	35	124
19Q LOSS WILD-TYPE	141	72	40

Figure S26. Get High-res Image Gene #74: '19q loss' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'22q loss' versus 'Time to Death'

P value = 2.92e-05 (logrank test), Q value = 0.018

Table S27. Gene #77: '22q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	427	75	0.0 - 211.2 (15.9)
22Q LOSS MUTATED	46	18	0.1 - 156.2 (16.9)
22Q LOSS WILD-TYPE	381	57	0.0 - 211.2 (15.7)

Figure S27. Get High-res Image Gene #77: '22q loss' versus Clinical Feature #1: 'Time to Death'

'22q loss' versus 'AGE'

P value = 5.45e-05 (Wilcoxon-test), Q value = 0.033

Table S28. Gene #77: '22q loss' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	429	43.0 (13.2)
22Q LOSS MUTATED	46	51.0 (13.9)
22Q LOSS WILD-TYPE	383	42.0 (12.9)

Figure S28. 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 = 430
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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