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

Brain Lower Grade Glioma (Primary solid tumor)

16 April 2014 | analyses__2014_04_16

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/C1VT1QR1

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 6 clinical features across 359 patients, 25 significant findings detected with Q value < 0.25.

1q gain cnv correlated to 'AGE'.
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'.
10p gain cnv correlated to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
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'.
6q loss cnv correlated to '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'.

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 6 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 25 significant findings detected.


		Clinical Features	Time to Death	AGE	GENDER	KARNOFSKY PERFORMANCE SCORE	HISTOLOGICAL TYPE	RADIATIONS RADIATION REGIMENINDICATION
	nCNV (%)	nWild-Type	logrank test	t-test	Fisher's exact test	t-test	Fisher's exact test	Fisher's exact test
10p loss	58 (16%)	301	0 (0)	7.19e-13 (3.31e-10)	0.25 (1.00)	0.00494 (1.00)	0.000346 (0.153)	0.508 (1.00)
10q loss	68 (19%)	291	1.25e-10 (5.71e-08)	1.99e-11 (9.13e-09)	0.225 (1.00)	0.0118 (1.00)	0.000157 (0.0699)	0.641 (1.00)
7p gain	85 (24%)	274	8.75e-05 (0.0392)	3.04e-06 (0.00138)	0.262 (1.00)	0.0209 (1.00)	0.107 (1.00)	0.393 (1.00)
7q gain	110 (31%)	249	0.000146 (0.0653)	5.01e-07 (0.000229)	0.358 (1.00)	0.138 (1.00)	0.0897 (1.00)	0.691 (1.00)
19q gain	18 (5%)	341	8.46e-06 (0.00383)	7.23e-05 (0.0325)	0.631 (1.00)	0.493 (1.00)	0.314 (1.00)	0.781 (1.00)
20p gain	34 (9%)	325	7.49e-07 (0.000341)	2.78e-06 (0.00126)	0.47 (1.00)	0.145 (1.00)	0.125 (1.00)	0.678 (1.00)
20q gain	35 (10%)	324	6.88e-07 (0.000314)	1.71e-05 (0.0077)	0.211 (1.00)	0.216 (1.00)	0.183 (1.00)	0.68 (1.00)
1q gain	15 (4%)	344	0.352 (1.00)	0.000432 (0.191)	0.117 (1.00)	0.263 (1.00)	0.266 (1.00)	0.54 (1.00)
3q gain	8 (2%)	351	0.000463 (0.204)	0.0543 (1.00)	0.478 (1.00)	0.383 (1.00)	0.0436 (1.00)	0.415 (1.00)
10p gain	33 (9%)	326	0.67 (1.00)	0.00479 (1.00)	0.0675 (1.00)	0.105 (1.00)	0.0111 (1.00)	0.00051 (0.224)
19p gain	69 (19%)	290	0.385 (1.00)	0.00588 (1.00)	0.503 (1.00)	0.111 (1.00)	6.21e-05 (0.0279)	0.877 (1.00)
1p loss	132 (37%)	227	0.00981 (1.00)	0.002 (0.856)	1 (1.00)	0.891 (1.00)	7.27e-30 (3.36e-27)	0.0158 (1.00)
6q loss	41 (11%)	318	0.000846 (0.37)	0.058 (1.00)	0.741 (1.00)	0.15 (1.00)	0.000565 (0.248)	0.0823 (1.00)
9p loss	78 (22%)	281	9.13e-05 (0.0408)	0.144 (1.00)	0.369 (1.00)	0.531 (1.00)	0.0434 (1.00)	0.0267 (1.00)
14q loss	55 (15%)	304	0.0002 (0.0888)	0.000788 (0.345)	0.66 (1.00)	0.102 (1.00)	0.221 (1.00)	0.403 (1.00)
19q loss	149 (42%)	210	0.136 (1.00)	0.0548 (1.00)	1 (1.00)	0.813 (1.00)	1.51e-26 (6.98e-24)	0.172 (1.00)
1p gain	10 (3%)	349	0.00287 (1.00)	0.0273 (1.00)	0.197 (1.00)	0.0205 (1.00)	0.00501 (1.00)	0.714 (1.00)
2p gain	7 (2%)	352	0.556 (1.00)	0.0732 (1.00)	0.707 (1.00)	0.479 (1.00)	0.504 (1.00)	0.685 (1.00)
2q gain	6 (2%)	353	0.909 (1.00)	0.155 (1.00)	0.42 (1.00)	0.479 (1.00)	0.292 (1.00)	0.64 (1.00)
3p gain	10 (3%)	349	0.00132 (0.575)	0.102 (1.00)	0.523 (1.00)	0.903 (1.00)	0.0312 (1.00)	0.714 (1.00)
4p gain	8 (2%)	351	0.289 (1.00)	0.953 (1.00)	0.297 (1.00)	0.709 (1.00)	0.0436 (1.00)	0.685 (1.00)
4q gain	3 (1%)	356	0.648 (1.00)	0.612 (1.00)	1 (1.00)		0.632 (1.00)	1 (1.00)
5p gain	7 (2%)	352	0.502 (1.00)	0.249 (1.00)	1 (1.00)	0.466 (1.00)	0.345 (1.00)	1 (1.00)
5q gain	5 (1%)	354	0.831 (1.00)	0.446 (1.00)	0.665 (1.00)	0.158 (1.00)	0.636 (1.00)	0.338 (1.00)
6p gain	6 (2%)	353	0.755 (1.00)	0.167 (1.00)	0.0982 (1.00)	0.0205 (1.00)	0.292 (1.00)	0.64 (1.00)
8p gain	31 (9%)	328	0.549 (1.00)	0.88 (1.00)	0.454 (1.00)	0.198 (1.00)	0.0812 (1.00)	1 (1.00)
8q gain	38 (11%)	321	0.509 (1.00)	0.326 (1.00)	0.492 (1.00)	0.0658 (1.00)	0.00344 (1.00)	0.843 (1.00)
9p gain	14 (4%)	345	0.0537 (1.00)	0.0291 (1.00)	0.0592 (1.00)	0.727 (1.00)	0.332 (1.00)	1 (1.00)
9q gain	19 (5%)	340	0.0356 (1.00)	0.0227 (1.00)	0.0168 (1.00)	0.725 (1.00)	0.0986 (1.00)	0.426 (1.00)
10q gain	5 (1%)	354	0.712 (1.00)	0.339 (1.00)	0.0648 (1.00)		0.103 (1.00)	0.0998 (1.00)
11p gain	25 (7%)	334	0.555 (1.00)	0.064 (1.00)	0.152 (1.00)	0.565 (1.00)	0.114 (1.00)	1 (1.00)
11q gain	41 (11%)	318	0.745 (1.00)	0.0668 (1.00)	0.0462 (1.00)	0.839 (1.00)	0.541 (1.00)	1 (1.00)
12p gain	26 (7%)	333	0.819 (1.00)	0.734 (1.00)	0.152 (1.00)	0.589 (1.00)	0.714 (1.00)	1 (1.00)
12q gain	12 (3%)	347	0.00159 (0.684)	0.248 (1.00)	0.155 (1.00)	0.514 (1.00)	1 (1.00)	0.737 (1.00)
13q gain	3 (1%)	356	0.529 (1.00)	0.818 (1.00)	0.596 (1.00)	0.468 (1.00)	0.28 (1.00)	1 (1.00)
14q gain	3 (1%)	356	0.469 (1.00)	0.391 (1.00)	1 (1.00)		1 (1.00)	0.153 (1.00)
15q gain	7 (2%)	352	0.103 (1.00)	0.00588 (1.00)	0.459 (1.00)	0.681 (1.00)	0.345 (1.00)	0.685 (1.00)
16p gain	13 (4%)	346	0.314 (1.00)	0.064 (1.00)	0.272 (1.00)	0.858 (1.00)	0.131 (1.00)	0.743 (1.00)
16q gain	13 (4%)	346	0.113 (1.00)	0.327 (1.00)	0.272 (1.00)	0.389 (1.00)	0.0351 (1.00)	0.323 (1.00)
17p gain	15 (4%)	344	0.041 (1.00)	0.284 (1.00)	0.429 (1.00)	0.169 (1.00)	0.0625 (1.00)	0.77 (1.00)
17q gain	16 (4%)	343	0.00554 (1.00)	0.318 (1.00)	0.307 (1.00)	0.86 (1.00)	0.181 (1.00)	1 (1.00)
18p gain	11 (3%)	348	0.0638 (1.00)	0.696 (1.00)	1 (1.00)	0.615 (1.00)	0.435 (1.00)	1 (1.00)
18q gain	8 (2%)	351	0.142 (1.00)	0.719 (1.00)	0.731 (1.00)	0.158 (1.00)	0.608 (1.00)	0.685 (1.00)
21q gain	20 (6%)	339	0.175 (1.00)	0.0168 (1.00)	0.819 (1.00)	0.276 (1.00)	0.476 (1.00)	1 (1.00)
22q gain	11 (3%)	348	0.949 (1.00)	0.115 (1.00)	0.76 (1.00)	0.978 (1.00)	0.0822 (1.00)	0.737 (1.00)
xq gain	27 (8%)	332	0.905 (1.00)	0.507 (1.00)	0.00911 (1.00)	0.666 (1.00)	0.187 (1.00)	0.643 (1.00)
1q loss	19 (5%)	340	0.92 (1.00)	0.0388 (1.00)	0.639 (1.00)	0.1 (1.00)	0.239 (1.00)	0.584 (1.00)
2p loss	13 (4%)	346	0.178 (1.00)	0.758 (1.00)	0.154 (1.00)	0.765 (1.00)	0.458 (1.00)	1 (1.00)
2q loss	13 (4%)	346	0.848 (1.00)	0.111 (1.00)	0.396 (1.00)	0.727 (1.00)	0.105 (1.00)	1 (1.00)
3p loss	15 (4%)	344	0.00894 (1.00)	0.659 (1.00)	0.429 (1.00)	0.0227 (1.00)	0.635 (1.00)	0.77 (1.00)
3q loss	20 (6%)	339	0.0139 (1.00)	0.87 (1.00)	0.065 (1.00)	0.241 (1.00)	0.878 (1.00)	0.597 (1.00)
4p loss	52 (14%)	307	0.891 (1.00)	0.00148 (0.641)	0.176 (1.00)	0.559 (1.00)	0.00169 (0.728)	0.489 (1.00)
4q loss	67 (19%)	292	0.882 (1.00)	0.174 (1.00)	0.222 (1.00)	0.631 (1.00)	0.0123 (1.00)	0.438 (1.00)
5p loss	27 (8%)	332	0.388 (1.00)	0.0887 (1.00)	1 (1.00)	0.238 (1.00)	0.0228 (1.00)	0.0199 (1.00)
5q loss	26 (7%)	333	0.0835 (1.00)	0.341 (1.00)	0.421 (1.00)	0.719 (1.00)	0.0901 (1.00)	0.0557 (1.00)
6p loss	22 (6%)	337	0.00091 (0.397)	0.388 (1.00)	0.665 (1.00)	0.344 (1.00)	0.0506 (1.00)	1 (1.00)
7p loss	3 (1%)	356	0.486 (1.00)	0.528 (1.00)	0.596 (1.00)		0.632 (1.00)	1 (1.00)
7q loss	3 (1%)	356	0.655 (1.00)	0.86 (1.00)	1 (1.00)	0.897 (1.00)	0.632 (1.00)	1 (1.00)
8p loss	12 (3%)	347	0.0444 (1.00)	0.151 (1.00)	1 (1.00)	0.543 (1.00)	0.262 (1.00)	0.501 (1.00)
8q loss	9 (3%)	350	0.0123 (1.00)	0.223 (1.00)	0.738 (1.00)	0.482 (1.00)	0.398 (1.00)	1 (1.00)
9q loss	31 (9%)	328	0.00515 (1.00)	0.234 (1.00)	0.708 (1.00)	0.0545 (1.00)	0.794 (1.00)	0.831 (1.00)
11p loss	45 (13%)	314	0.313 (1.00)	0.214 (1.00)	0.201 (1.00)	0.995 (1.00)	0.0578 (1.00)	0.467 (1.00)
11q loss	16 (4%)	343	0.0113 (1.00)	0.073 (1.00)	0.801 (1.00)	0.135 (1.00)	0.0803 (1.00)	0.376 (1.00)
12p loss	15 (4%)	344	0.8 (1.00)	0.229 (1.00)	0.604 (1.00)	0.941 (1.00)	0.334 (1.00)	0.54 (1.00)
12q loss	31 (9%)	328	0.921 (1.00)	0.362 (1.00)	0.574 (1.00)	0.564 (1.00)	0.0679 (1.00)	0.383 (1.00)
13q loss	84 (23%)	275	0.251 (1.00)	0.685 (1.00)	0.171 (1.00)	0.293 (1.00)	0.687 (1.00)	0.0213 (1.00)
15q loss	32 (9%)	327	0.2 (1.00)	0.474 (1.00)	0.854 (1.00)	0.714 (1.00)	0.466 (1.00)	1 (1.00)
16p loss	9 (3%)	350	0.21 (1.00)	0.00397 (1.00)	0.515 (1.00)	0.0772 (1.00)	0.836 (1.00)	1 (1.00)
16q loss	16 (4%)	343	0.148 (1.00)	0.00486 (1.00)	0.801 (1.00)	0.892 (1.00)	0.769 (1.00)	0.557 (1.00)
17p loss	12 (3%)	347	0.0163 (1.00)	0.0357 (1.00)	0.238 (1.00)	0.025 (1.00)	0.534 (1.00)	0.307 (1.00)
17q loss	8 (2%)	351	0.415 (1.00)	0.11 (1.00)	0.478 (1.00)	0.156 (1.00)	0.674 (1.00)	0.685 (1.00)
18p loss	51 (14%)	308	0.704 (1.00)	0.0313 (1.00)	0.033 (1.00)	0.666 (1.00)	0.402 (1.00)	0.726 (1.00)
18q loss	47 (13%)	312	0.797 (1.00)	0.0788 (1.00)	0.161 (1.00)	0.74 (1.00)	0.312 (1.00)	1 (1.00)
19p loss	18 (5%)	341	0.341 (1.00)	0.62 (1.00)	0.81 (1.00)	0.561 (1.00)	0.911 (1.00)	0.166 (1.00)
20p loss	3 (1%)	356	0.511 (1.00)	0.486 (1.00)	0.596 (1.00)		1 (1.00)	0.576 (1.00)
21q loss	20 (6%)	339	0.662 (1.00)	0.61 (1.00)	0.249 (1.00)	0.0804 (1.00)	0.101 (1.00)	0.792 (1.00)
22q loss	39 (11%)	320	0.00136 (0.59)	0.00142 (0.614)	0.5 (1.00)	0.00792 (1.00)	0.168 (1.00)	1 (1.00)
xq loss	47 (13%)	312	0.0451 (1.00)	0.23 (1.00)	0.641 (1.00)	0.487 (1.00)	0.461 (1.00)	0.858 (1.00)

'1q gain' versus 'AGE'

P value = 0.000432 (t-test), Q value = 0.19

Table S1. Gene #2: '1q gain' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	359	43.6 (13.5)
1Q GAIN MUTATED	15	55.8 (10.8)
1Q GAIN WILD-TYPE	344	43.1 (13.4)

Figure S1. Get High-res Image Gene #2: '1q gain' versus Clinical Feature #2: 'AGE'

'3q gain' versus 'Time to Death'

P value = 0.000463 (logrank test), Q value = 0.2

Table S2. Gene #6: '3q gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	356	68	0.0 - 211.2 (14.8)
3Q GAIN MUTATED	8	4	0.2 - 47.8 (9.1)
3Q GAIN WILD-TYPE	348	64	0.0 - 211.2 (14.9)

Figure S2. Get High-res Image Gene #6: '3q gain' versus Clinical Feature #1: 'Time to Death'

'7p gain' versus 'Time to Death'

P value = 8.75e-05 (logrank test), Q value = 0.039

Table S3. Gene #12: '7p gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	356	68	0.0 - 211.2 (14.8)
7P GAIN MUTATED	85	30	0.1 - 211.2 (13.7)
7P GAIN WILD-TYPE	271	38	0.0 - 182.3 (15.0)

Figure S3. Get High-res Image Gene #12: '7p gain' versus Clinical Feature #1: 'Time to Death'

'7p gain' versus 'AGE'

P value = 3.04e-06 (t-test), Q value = 0.0014

Table S4. Gene #12: '7p gain' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	359	43.6 (13.5)
7P GAIN MUTATED	85	49.7 (13.3)
7P GAIN WILD-TYPE	274	41.7 (13.0)

Figure S4. Get High-res Image Gene #12: '7p gain' versus Clinical Feature #2: 'AGE'

'7q gain' versus 'Time to Death'

P value = 0.000146 (logrank test), Q value = 0.065

Table S5. Gene #13: '7q gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	356	68	0.0 - 211.2 (14.8)
7Q GAIN MUTATED	108	35	0.1 - 211.2 (15.0)
7Q GAIN WILD-TYPE	248	33	0.0 - 182.3 (14.8)

Figure S5. Get High-res Image Gene #13: '7q gain' versus Clinical Feature #1: 'Time to Death'

'7q gain' versus 'AGE'

P value = 5.01e-07 (t-test), Q value = 0.00023

Table S6. Gene #13: '7q gain' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	359	43.6 (13.5)
7Q GAIN MUTATED	110	49.1 (13.5)
7Q GAIN WILD-TYPE	249	41.2 (12.8)

Figure S6. Get High-res Image Gene #13: '7q gain' versus Clinical Feature #2: 'AGE'

'10p gain' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 0.00051 (Fisher's exact test), Q value = 0.22

Table S7. Gene #18: '10p gain' versus Clinical Feature #6: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients	NO	YES
ALL	89	270
10P GAIN MUTATED	17	16
10P GAIN WILD-TYPE	72	254

Figure S7. Get High-res Image Gene #18: '10p gain' versus Clinical Feature #6: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'19p gain' versus 'HISTOLOGICAL.TYPE'

P value = 6.21e-05 (Fisher's exact test), Q value = 0.028

Table S8. Gene #33: '19p gain' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	123	99	137
19P GAIN MUTATED	12	15	42
19P GAIN WILD-TYPE	111	84	95

Figure S8. Get High-res Image Gene #33: '19p gain' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'19q gain' versus 'Time to Death'

P value = 8.46e-06 (logrank test), Q value = 0.0038

Table S9. Gene #34: '19q gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	356	68	0.0 - 211.2 (14.8)
19Q GAIN MUTATED	18	7	0.5 - 49.5 (11.8)
19Q GAIN WILD-TYPE	338	61	0.0 - 211.2 (15.0)

Figure S9. Get High-res Image Gene #34: '19q gain' versus Clinical Feature #1: 'Time to Death'

'19q gain' versus 'AGE'

P value = 7.23e-05 (t-test), Q value = 0.032

Table S10. Gene #34: '19q gain' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	359	43.6 (13.5)
19Q GAIN MUTATED	18	56.3 (10.9)
19Q GAIN WILD-TYPE	341	42.9 (13.3)

Figure S10. Get High-res Image Gene #34: '19q gain' versus Clinical Feature #2: 'AGE'

'20p gain' versus 'Time to Death'

P value = 7.49e-07 (logrank test), Q value = 0.00034

Table S11. Gene #35: '20p gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	356	68	0.0 - 211.2 (14.8)
20P GAIN MUTATED	34	12	0.5 - 49.5 (11.8)
20P GAIN WILD-TYPE	322	56	0.0 - 211.2 (15.0)

Figure S11. Get High-res Image Gene #35: '20p gain' versus Clinical Feature #1: 'Time to Death'

'20p gain' versus 'AGE'

P value = 2.78e-06 (t-test), Q value = 0.0013

Table S12. Gene #35: '20p gain' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	359	43.6 (13.5)
20P GAIN MUTATED	34	54.9 (12.7)
20P GAIN WILD-TYPE	325	42.4 (13.0)

Figure S12. Get High-res Image Gene #35: '20p gain' versus Clinical Feature #2: 'AGE'

'20q gain' versus 'Time to Death'

P value = 6.88e-07 (logrank test), Q value = 0.00031

Table S13. Gene #36: '20q gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	356	68	0.0 - 211.2 (14.8)
20Q GAIN MUTATED	35	12	0.5 - 49.5 (12.2)
20Q GAIN WILD-TYPE	321	56	0.0 - 211.2 (15.0)

Figure S13. Get High-res Image Gene #36: '20q gain' versus Clinical Feature #1: 'Time to Death'

'20q gain' versus 'AGE'

P value = 1.71e-05 (t-test), Q value = 0.0077

Table S14. Gene #36: '20q gain' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	359	43.6 (13.5)
20Q GAIN MUTATED	35	54.1 (13.5)
20Q GAIN WILD-TYPE	324	42.5 (13.0)

Figure S14. Get High-res Image Gene #36: '20q gain' versus Clinical Feature #2: 'AGE'

'1p loss' versus 'HISTOLOGICAL.TYPE'

P value = 7.27e-30 (Fisher's exact test), Q value = 3.4e-27

Table S15. Gene #40: '1p loss' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	123	99	137
1P LOSS MUTATED	7	28	97
1P LOSS WILD-TYPE	116	71	40

Figure S15. Get High-res Image Gene #40: '1p loss' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'6q loss' versus 'HISTOLOGICAL.TYPE'

P value = 0.000565 (Fisher's exact test), Q value = 0.25

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

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	123	99	137
6Q LOSS MUTATED	25	9	7
6Q LOSS WILD-TYPE	98	90	130

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

'9p loss' versus 'Time to Death'

P value = 9.13e-05 (logrank test), Q value = 0.041

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

	nPatients	nDeath	Duration Range (Median), Month
ALL	356	68	0.0 - 211.2 (14.8)
9P LOSS MUTATED	78	25	0.1 - 117.4 (16.1)
9P LOSS WILD-TYPE	278	43	0.0 - 211.2 (14.5)

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	356	68	0.0 - 211.2 (14.8)
10P LOSS MUTATED	58	28	0.1 - 134.3 (11.4)
10P LOSS WILD-TYPE	298	40	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 = 7.19e-13 (t-test), Q value = 3.3e-10

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

	nPatients	Mean (Std.Dev)
ALL	359	43.6 (13.5)
10P LOSS MUTATED	58	55.4 (11.4)
10P LOSS WILD-TYPE	301	41.3 (12.7)

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

'10p loss' versus 'HISTOLOGICAL.TYPE'

P value = 0.000346 (Fisher's exact test), Q value = 0.15

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

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	123	99	137
10P LOSS MUTATED	33	13	12
10P LOSS WILD-TYPE	90	86	125

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

'10q loss' versus 'Time to Death'

P value = 1.25e-10 (logrank test), Q value = 5.7e-08

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

	nPatients	nDeath	Duration Range (Median), Month
ALL	356	68	0.0 - 211.2 (14.8)
10Q LOSS MUTATED	67	32	0.1 - 156.2 (12.2)
10Q LOSS WILD-TYPE	289	36	0.0 - 211.2 (15.1)

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

'10q loss' versus 'AGE'

P value = 1.99e-11 (t-test), Q value = 9.1e-09

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

	nPatients	Mean (Std.Dev)
ALL	359	43.6 (13.5)
10Q LOSS MUTATED	68	54.0 (12.6)
10Q LOSS WILD-TYPE	291	41.2 (12.5)

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

'10q loss' versus 'HISTOLOGICAL.TYPE'

P value = 0.000157 (Fisher's exact test), Q value = 0.07

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

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	123	99	137
10Q LOSS MUTATED	38	15	15
10Q LOSS WILD-TYPE	85	84	122

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

'14q loss' versus 'Time to Death'

P value = 2e-04 (logrank test), Q value = 0.089

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

	nPatients	nDeath	Duration Range (Median), Month
ALL	356	68	0.0 - 211.2 (14.8)
14Q LOSS MUTATED	54	19	0.2 - 130.8 (15.0)
14Q LOSS WILD-TYPE	302	49	0.0 - 211.2 (14.7)

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

'19q loss' versus 'HISTOLOGICAL.TYPE'

P value = 1.51e-26 (Fisher's exact test), Q value = 7e-24

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

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	123	99	137
19Q LOSS MUTATED	15	31	103
19Q LOSS WILD-TYPE	108	68	34

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

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Clinical data file = LGG-TP.merged_data.txt
Number of patients = 359
Number of significantly arm-level cnvs = 78
Number of selected clinical features = 6
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

Student's t-test analysis

For continuous numerical clinical features, two-tailed Student's t test with unequal variance (Lehmann and Romano 2005) was applied to compare the clinical values between tumors with and without gene mutations using 't.test' 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] Lehmann and Romano, Testing Statistical Hypotheses (3E ed.), New York: Springer. ISBN 0387988645 (2005)

[3] 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)

[4] 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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