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

Brain Lower Grade Glioma (Primary solid tumor)

23 September 2013 | analyses__2013_09_23

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 (2013): Correlation between copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1X34VQR

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 71 arm-level events and 6 clinical features across 229 patients, 19 significant findings detected with Q value < 0.25.

3Q GAIN MUTATION ANALYSIS cnv correlated to 'Time to Death'.
7Q GAIN MUTATION ANALYSIS cnv correlated to 'AGE'.
19Q GAIN MUTATION ANALYSIS cnv correlated to 'Time to Death' and 'AGE'.
20P GAIN MUTATION ANALYSIS cnv correlated to 'Time to Death' and 'AGE'.
20Q GAIN MUTATION ANALYSIS cnv correlated to 'Time to Death' and 'AGE'.
1P LOSS MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.
10P LOSS MUTATION ANALYSIS cnv correlated to 'Time to Death', 'AGE', and 'HISTOLOGICAL.TYPE'.
10Q LOSS MUTATION ANALYSIS cnv correlated to 'Time to Death', 'AGE', and 'HISTOLOGICAL.TYPE'.
11Q LOSS MUTATION ANALYSIS cnv correlated to 'Time to Death'.
17P LOSS MUTATION ANALYSIS cnv correlated to 'Time to Death' and 'AGE'.
19Q LOSS MUTATION ANALYSIS 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 71 arm-level events and 6 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 19 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 MUTATION ANALYSIS	39 (17%)	190	1.15e-12 (4.84e-10)	1.43e-08 (5.97e-06)	0.0219 (1.00)	0.305 (1.00)	0.000156 (0.0639)	0.473 (1.00)
10Q LOSS MUTATION ANALYSIS	47 (21%)	182	5.03e-06 (0.00209)	2.25e-07 (9.36e-05)	0.022 (1.00)	0.644 (1.00)	0.000297 (0.12)	0.738 (1.00)
19Q GAIN MUTATION ANALYSIS	11 (5%)	218	5.1e-05 (0.021)	0.00058 (0.234)	0.758 (1.00)	0.243 (1.00)	0.455 (1.00)	0.349 (1.00)
20P GAIN MUTATION ANALYSIS	22 (10%)	207	9.19e-07 (0.000382)	8.28e-05 (0.034)	0.178 (1.00)	0.746 (1.00)	0.354 (1.00)	0.5 (1.00)
20Q GAIN MUTATION ANALYSIS	22 (10%)	207	2.34e-05 (0.00969)	0.00025 (0.102)	0.0717 (1.00)	0.841 (1.00)	0.515 (1.00)	0.5 (1.00)
17P LOSS MUTATION ANALYSIS	10 (4%)	219	0.000276 (0.112)	0.000572 (0.231)	0.114 (1.00)	0.142 (1.00)	0.849 (1.00)	0.323 (1.00)
3Q GAIN MUTATION ANALYSIS	7 (3%)	222	0.000245 (0.0998)	0.0857 (1.00)	0.703 (1.00)	0.273 (1.00)	0.0708 (1.00)	0.438 (1.00)
7Q GAIN MUTATION ANALYSIS	68 (30%)	161	0.00349 (1.00)	8.53e-05 (0.035)	0.192 (1.00)	0.605 (1.00)	0.188 (1.00)	0.768 (1.00)
1P LOSS MUTATION ANALYSIS	76 (33%)	153	0.0678 (1.00)	0.0285 (1.00)	1 (1.00)	0.647 (1.00)	9.42e-18 (3.97e-15)	0.0616 (1.00)
11Q LOSS MUTATION ANALYSIS	9 (4%)	220	4.94e-05 (0.0204)	0.159 (1.00)	0.192 (1.00)	0.439 (1.00)	0.14 (1.00)	0.488 (1.00)
19Q LOSS MUTATION ANALYSIS	87 (38%)	142	0.161 (1.00)	0.186 (1.00)	0.495 (1.00)	0.882 (1.00)	6.56e-14 (2.75e-11)	0.405 (1.00)
1P GAIN MUTATION ANALYSIS	8 (3%)	221	0.00145 (0.58)	0.0897 (1.00)	0.144 (1.00)	0.0763 (1.00)	0.00267 (1.00)	1 (1.00)
1Q GAIN MUTATION ANALYSIS	12 (5%)	217	0.828 (1.00)	0.00363 (1.00)	0.14 (1.00)	0.44 (1.00)	0.134 (1.00)	1 (1.00)
2P GAIN MUTATION ANALYSIS	5 (2%)	224	0.865 (1.00)	0.259 (1.00)	0.658 (1.00)	0.353 (1.00)	0.522 (1.00)	1 (1.00)
2Q GAIN MUTATION ANALYSIS	5 (2%)	224	0.865 (1.00)	0.259 (1.00)	0.658 (1.00)	0.353 (1.00)	0.522 (1.00)	1 (1.00)
3P GAIN MUTATION ANALYSIS	7 (3%)	222	0.0109 (1.00)	0.0901 (1.00)	0.247 (1.00)	0.704 (1.00)	0.159 (1.00)	1 (1.00)
6P GAIN MUTATION ANALYSIS	4 (2%)	225	0.751 (1.00)	0.341 (1.00)	1 (1.00)	0.0763 (1.00)	0.487 (1.00)	0.647 (1.00)
6Q GAIN MUTATION ANALYSIS	3 (1%)	226	0.712 (1.00)	0.666 (1.00)	0.587 (1.00)	0.0763 (1.00)	0.487 (1.00)	0.563 (1.00)
7P GAIN MUTATION ANALYSIS	54 (24%)	175	0.00683 (1.00)	0.00193 (0.772)	0.0844 (1.00)	0.876 (1.00)	0.17 (1.00)	0.874 (1.00)
8P GAIN MUTATION ANALYSIS	22 (10%)	207	0.609 (1.00)	0.447 (1.00)	0.261 (1.00)	0.978 (1.00)	0.138 (1.00)	0.822 (1.00)
8Q GAIN MUTATION ANALYSIS	27 (12%)	202	0.884 (1.00)	0.106 (1.00)	0.225 (1.00)	0.554 (1.00)	0.0278 (1.00)	0.837 (1.00)
9P GAIN MUTATION ANALYSIS	8 (3%)	221	0.021 (1.00)	0.102 (1.00)	0.144 (1.00)	0.5 (1.00)	0.547 (1.00)	1 (1.00)
9Q GAIN MUTATION ANALYSIS	9 (4%)	220	0.00693 (1.00)	0.0708 (1.00)	0.0118 (1.00)	0.788 (1.00)	0.479 (1.00)	1 (1.00)
10P GAIN MUTATION ANALYSIS	25 (11%)	204	0.645 (1.00)	0.0345 (1.00)	0.0904 (1.00)	0.0594 (1.00)	0.0641 (1.00)	0.00393 (1.00)
10Q GAIN MUTATION ANALYSIS	3 (1%)	226	0.414 (1.00)	0.113 (1.00)	0.256 (1.00)		0.0507 (1.00)	0.0595 (1.00)
11P GAIN MUTATION ANALYSIS	17 (7%)	212	0.892 (1.00)	0.0255 (1.00)	0.613 (1.00)	0.884 (1.00)	0.409 (1.00)	0.801 (1.00)
11Q GAIN MUTATION ANALYSIS	25 (11%)	204	0.489 (1.00)	0.0185 (1.00)	0.832 (1.00)	0.973 (1.00)	0.492 (1.00)	1 (1.00)
12P GAIN MUTATION ANALYSIS	16 (7%)	213	0.53 (1.00)	0.147 (1.00)	0.307 (1.00)	0.0763 (1.00)	1 (1.00)	1 (1.00)
12Q GAIN MUTATION ANALYSIS	8 (3%)	221	0.0586 (1.00)	0.721 (1.00)	1 (1.00)	0.0763 (1.00)	0.815 (1.00)	0.485 (1.00)
15Q GAIN MUTATION ANALYSIS	5 (2%)	224	0.48 (1.00)	0.14 (1.00)	0.385 (1.00)	0.666 (1.00)	0.617 (1.00)	1 (1.00)
16P GAIN MUTATION ANALYSIS	7 (3%)	222	0.433 (1.00)	0.136 (1.00)	0.247 (1.00)		0.425 (1.00)	0.707 (1.00)
16Q GAIN MUTATION ANALYSIS	9 (4%)	220	0.149 (1.00)	0.157 (1.00)	0.517 (1.00)	0.771 (1.00)	0.0946 (1.00)	0.741 (1.00)
17P GAIN MUTATION ANALYSIS	5 (2%)	224	0.198 (1.00)	0.495 (1.00)	0.385 (1.00)	0.704 (1.00)	0.278 (1.00)	0.0795 (1.00)
17Q GAIN MUTATION ANALYSIS	5 (2%)	224	0.198 (1.00)	0.495 (1.00)	0.385 (1.00)	0.704 (1.00)	0.278 (1.00)	0.0795 (1.00)
18P GAIN MUTATION ANALYSIS	9 (4%)	220	0.315 (1.00)	0.9 (1.00)	1 (1.00)	0.0763 (1.00)	0.291 (1.00)	0.488 (1.00)
18Q GAIN MUTATION ANALYSIS	6 (3%)	223	0.0455 (1.00)	0.502 (1.00)	1 (1.00)		0.44 (1.00)	0.407 (1.00)
19P GAIN MUTATION ANALYSIS	36 (16%)	193	0.416 (1.00)	0.00344 (1.00)	1 (1.00)	0.796 (1.00)	0.127 (1.00)	1 (1.00)
21Q GAIN MUTATION ANALYSIS	10 (4%)	219	0.966 (1.00)	0.484 (1.00)	0.755 (1.00)		0.105 (1.00)	1 (1.00)
22Q GAIN MUTATION ANALYSIS	7 (3%)	222	0.295 (1.00)	0.212 (1.00)	0.703 (1.00)	0.704 (1.00)	0.0611 (1.00)	1 (1.00)
XQ GAIN MUTATION ANALYSIS	18 (8%)	211	0.559 (1.00)	0.165 (1.00)	0.0813 (1.00)	0.836 (1.00)	0.234 (1.00)	0.451 (1.00)
1Q LOSS MUTATION ANALYSIS	14 (6%)	215	0.726 (1.00)	0.152 (1.00)	0.409 (1.00)	0.289 (1.00)	0.0463 (1.00)	0.784 (1.00)
2P LOSS MUTATION ANALYSIS	9 (4%)	220	0.138 (1.00)	0.701 (1.00)	0.305 (1.00)	0.0625 (1.00)	0.479 (1.00)	0.741 (1.00)
2Q LOSS MUTATION ANALYSIS	7 (3%)	222	0.501 (1.00)	0.00747 (1.00)	0.466 (1.00)	0.166 (1.00)	0.267 (1.00)	1 (1.00)
3P LOSS MUTATION ANALYSIS	9 (4%)	220	0.122 (1.00)	0.0584 (1.00)	0.305 (1.00)	0.958 (1.00)	0.914 (1.00)	0.741 (1.00)
3Q LOSS MUTATION ANALYSIS	15 (7%)	214	0.107 (1.00)	0.836 (1.00)	0.185 (1.00)	0.271 (1.00)	0.748 (1.00)	1 (1.00)
4P LOSS MUTATION ANALYSIS	37 (16%)	192	0.735 (1.00)	0.0494 (1.00)	0.278 (1.00)	0.554 (1.00)	0.0913 (1.00)	0.587 (1.00)
4Q LOSS MUTATION ANALYSIS	46 (20%)	183	0.306 (1.00)	0.424 (1.00)	0.507 (1.00)	0.61 (1.00)	0.0566 (1.00)	0.866 (1.00)
5P LOSS MUTATION ANALYSIS	19 (8%)	210	0.497 (1.00)	0.0974 (1.00)	0.147 (1.00)	0.362 (1.00)	0.038 (1.00)	0.047 (1.00)
5Q LOSS MUTATION ANALYSIS	17 (7%)	212	0.137 (1.00)	0.819 (1.00)	0.806 (1.00)	0.0687 (1.00)	0.565 (1.00)	0.0372 (1.00)
6P LOSS MUTATION ANALYSIS	14 (6%)	215	0.0214 (1.00)	0.586 (1.00)	0.784 (1.00)	0.319 (1.00)	0.0252 (1.00)	0.574 (1.00)
6Q LOSS MUTATION ANALYSIS	29 (13%)	200	0.00389 (1.00)	0.124 (1.00)	0.113 (1.00)	0.166 (1.00)	0.00422 (1.00)	0.314 (1.00)
8P LOSS MUTATION ANALYSIS	8 (3%)	221	0.124 (1.00)	0.112 (1.00)	1 (1.00)	0.824 (1.00)	0.243 (1.00)	0.715 (1.00)
8Q LOSS MUTATION ANALYSIS	6 (3%)	223	0.00478 (1.00)	0.0997 (1.00)	0.411 (1.00)	0.824 (1.00)	0.216 (1.00)	1 (1.00)
9P LOSS MUTATION ANALYSIS	55 (24%)	174	0.0098 (1.00)	0.053 (1.00)	0.534 (1.00)	0.74 (1.00)	0.104 (1.00)	0.113 (1.00)
9Q LOSS MUTATION ANALYSIS	22 (10%)	207	0.0403 (1.00)	0.0402 (1.00)	1 (1.00)	0.158 (1.00)	0.47 (1.00)	0.822 (1.00)
11P LOSS MUTATION ANALYSIS	28 (12%)	201	0.451 (1.00)	0.308 (1.00)	0.162 (1.00)	0.731 (1.00)	0.0929 (1.00)	0.417 (1.00)
12P LOSS MUTATION ANALYSIS	13 (6%)	216	0.539 (1.00)	0.2 (1.00)	0.571 (1.00)	0.345 (1.00)	0.333 (1.00)	1 (1.00)
12Q LOSS MUTATION ANALYSIS	21 (9%)	208	0.348 (1.00)	0.307 (1.00)	1 (1.00)	0.667 (1.00)	0.304 (1.00)	0.484 (1.00)
13Q LOSS MUTATION ANALYSIS	59 (26%)	170	0.769 (1.00)	0.248 (1.00)	0.544 (1.00)	0.362 (1.00)	0.2 (1.00)	0.0888 (1.00)
14Q LOSS MUTATION ANALYSIS	37 (16%)	192	0.00103 (0.414)	0.0208 (1.00)	0.373 (1.00)	0.198 (1.00)	0.289 (1.00)	0.714 (1.00)
15Q LOSS MUTATION ANALYSIS	19 (8%)	210	0.464 (1.00)	0.931 (1.00)	0.631 (1.00)	0.811 (1.00)	0.83 (1.00)	0.81 (1.00)
16P LOSS MUTATION ANALYSIS	7 (3%)	222	0.408 (1.00)	0.0647 (1.00)	1 (1.00)	0.439 (1.00)	0.425 (1.00)	0.438 (1.00)
16Q LOSS MUTATION ANALYSIS	12 (5%)	217	0.275 (1.00)	0.0195 (1.00)	0.379 (1.00)	0.619 (1.00)	0.361 (1.00)	0.546 (1.00)
17Q LOSS MUTATION ANALYSIS	7 (3%)	222	0.0228 (1.00)	0.0181 (1.00)	0.703 (1.00)	0.319 (1.00)	0.721 (1.00)	0.707 (1.00)
18P LOSS MUTATION ANALYSIS	27 (12%)	202	0.563 (1.00)	0.709 (1.00)	0.225 (1.00)	0.548 (1.00)	0.813 (1.00)	0.675 (1.00)
18Q LOSS MUTATION ANALYSIS	28 (12%)	201	0.304 (1.00)	0.663 (1.00)	0.686 (1.00)	0.852 (1.00)	0.565 (1.00)	0.685 (1.00)
19P LOSS MUTATION ANALYSIS	13 (6%)	216	0.88 (1.00)	0.197 (1.00)	0.777 (1.00)	0.352 (1.00)	0.937 (1.00)	0.141 (1.00)
20P LOSS MUTATION ANALYSIS	3 (1%)	226	0.485 (1.00)	0.545 (1.00)	0.587 (1.00)		1 (1.00)	1 (1.00)
21Q LOSS MUTATION ANALYSIS	19 (8%)	210	0.318 (1.00)	0.429 (1.00)	0.238 (1.00)	0.257 (1.00)	0.0193 (1.00)	0.625 (1.00)
22Q LOSS MUTATION ANALYSIS	25 (11%)	204	0.0462 (1.00)	0.0478 (1.00)	0.0179 (1.00)	0.208 (1.00)	0.0196 (1.00)	0.83 (1.00)
XQ LOSS MUTATION ANALYSIS	31 (14%)	198	0.141 (1.00)	0.411 (1.00)	1 (1.00)	0.998 (1.00)	0.298 (1.00)	1 (1.00)

'3Q GAIN MUTATION STATUS' versus 'Time to Death'

P value = 0.000245 (logrank test), Q value = 0.1

Table S1. Gene #6: '3Q GAIN MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	229	55	0.0 - 211.2 (14.5)
3Q GAIN MUTATED	7	4	0.2 - 41.1 (8.8)
3Q GAIN WILD-TYPE	222	51	0.0 - 211.2 (14.5)

Figure S1. Get High-res Image Gene #6: '3Q GAIN MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'7Q GAIN MUTATION STATUS' versus 'AGE'

P value = 8.53e-05 (t-test), Q value = 0.035

Table S2. Gene #10: '7Q GAIN MUTATION STATUS' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	229	42.8 (13.4)
7Q GAIN MUTATED	68	48.2 (13.4)
7Q GAIN WILD-TYPE	161	40.5 (12.7)

Figure S2. Get High-res Image Gene #10: '7Q GAIN MUTATION STATUS' versus Clinical Feature #2: 'AGE'

'19Q GAIN MUTATION STATUS' versus 'Time to Death'

P value = 5.1e-05 (logrank test), Q value = 0.021

Table S3. Gene #29: '19Q GAIN MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	229	55	0.0 - 211.2 (14.5)
19Q GAIN MUTATED	11	5	0.5 - 26.3 (12.2)
19Q GAIN WILD-TYPE	218	50	0.0 - 211.2 (14.7)

Figure S3. Get High-res Image Gene #29: '19Q GAIN MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'19Q GAIN MUTATION STATUS' versus 'AGE'

P value = 0.00058 (t-test), Q value = 0.23

Table S4. Gene #29: '19Q GAIN MUTATION STATUS' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	229	42.8 (13.4)
19Q GAIN MUTATED	11	54.4 (8.4)
19Q GAIN WILD-TYPE	218	42.2 (13.3)

Figure S4. Get High-res Image Gene #29: '19Q GAIN MUTATION STATUS' versus Clinical Feature #2: 'AGE'

'20P GAIN MUTATION STATUS' versus 'Time to Death'

P value = 9.19e-07 (logrank test), Q value = 0.00038

Table S5. Gene #30: '20P GAIN MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	229	55	0.0 - 211.2 (14.5)
20P GAIN MUTATED	22	9	0.5 - 41.1 (12.2)
20P GAIN WILD-TYPE	207	46	0.0 - 211.2 (14.9)

Figure S5. Get High-res Image Gene #30: '20P GAIN MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'20P GAIN MUTATION STATUS' versus 'AGE'

P value = 8.28e-05 (t-test), Q value = 0.034

Table S6. Gene #30: '20P GAIN MUTATION STATUS' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	229	42.8 (13.4)
20P GAIN MUTATED	22	52.3 (9.9)
20P GAIN WILD-TYPE	207	41.8 (13.3)

Figure S6. Get High-res Image Gene #30: '20P GAIN MUTATION STATUS' versus Clinical Feature #2: 'AGE'

'20Q GAIN MUTATION STATUS' versus 'Time to Death'

P value = 2.34e-05 (logrank test), Q value = 0.0097

Table S7. Gene #31: '20Q GAIN MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	229	55	0.0 - 211.2 (14.5)
20Q GAIN MUTATED	22	8	0.5 - 41.1 (12.2)
20Q GAIN WILD-TYPE	207	47	0.0 - 211.2 (14.9)

Figure S7. Get High-res Image Gene #31: '20Q GAIN MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'20Q GAIN MUTATION STATUS' versus 'AGE'

P value = 0.00025 (t-test), Q value = 0.1

Table S8. Gene #31: '20Q GAIN MUTATION STATUS' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	229	42.8 (13.4)
20Q GAIN MUTATED	22	51.9 (10.5)
20Q GAIN WILD-TYPE	207	41.8 (13.3)

Figure S8. Get High-res Image Gene #31: '20Q GAIN MUTATION STATUS' versus Clinical Feature #2: 'AGE'

'1P LOSS MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 9.42e-18 (Fisher's exact test), Q value = 4e-15

Table S9. Gene #35: '1P LOSS MUTATION STATUS' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	71	64	93
1P LOSS MUTATED	5	10	61
1P LOSS WILD-TYPE	66	54	32

Figure S9. Get High-res Image Gene #35: '1P LOSS MUTATION STATUS' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'10P LOSS MUTATION STATUS' versus 'Time to Death'

P value = 1.15e-12 (logrank test), Q value = 4.8e-10

Table S10. Gene #51: '10P LOSS MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	229	55	0.0 - 211.2 (14.5)
10P LOSS MUTATED	39	20	0.1 - 134.3 (10.4)
10P LOSS WILD-TYPE	190	35	0.0 - 211.2 (15.2)

Figure S10. Get High-res Image Gene #51: '10P LOSS MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'10P LOSS MUTATION STATUS' versus 'AGE'

P value = 1.43e-08 (t-test), Q value = 6e-06

Table S11. Gene #51: '10P LOSS MUTATION STATUS' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	229	42.8 (13.4)
10P LOSS MUTATED	39	53.7 (11.1)
10P LOSS WILD-TYPE	190	40.5 (12.7)

Figure S11. Get High-res Image Gene #51: '10P LOSS MUTATION STATUS' versus Clinical Feature #2: 'AGE'

'10P LOSS MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 0.000156 (Fisher's exact test), Q value = 0.064

Table S12. Gene #51: '10P LOSS MUTATION STATUS' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	71	64	93
10P LOSS MUTATED	23	9	7
10P LOSS WILD-TYPE	48	55	86

Figure S12. Get High-res Image Gene #51: '10P LOSS MUTATION STATUS' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'10Q LOSS MUTATION STATUS' versus 'Time to Death'

P value = 5.03e-06 (logrank test), Q value = 0.0021

Table S13. Gene #52: '10Q LOSS MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	229	55	0.0 - 211.2 (14.5)
10Q LOSS MUTATED	47	25	0.1 - 156.2 (12.2)
10Q LOSS WILD-TYPE	182	30	0.0 - 211.2 (14.9)

Figure S13. Get High-res Image Gene #52: '10Q LOSS MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'10Q LOSS MUTATION STATUS' versus 'AGE'

P value = 2.25e-07 (t-test), Q value = 9.4e-05

Table S14. Gene #52: '10Q LOSS MUTATION STATUS' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	229	42.8 (13.4)
10Q LOSS MUTATED	47	52.0 (12.3)
10Q LOSS WILD-TYPE	182	40.4 (12.6)

Figure S14. Get High-res Image Gene #52: '10Q LOSS MUTATION STATUS' versus Clinical Feature #2: 'AGE'

'10Q LOSS MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 0.000297 (Fisher's exact test), Q value = 0.12

Table S15. Gene #52: '10Q LOSS MUTATION STATUS' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	71	64	93
10Q LOSS MUTATED	26	11	10
10Q LOSS WILD-TYPE	45	53	83

Figure S15. Get High-res Image Gene #52: '10Q LOSS MUTATION STATUS' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'11Q LOSS MUTATION STATUS' versus 'Time to Death'

P value = 4.94e-05 (logrank test), Q value = 0.02

Table S16. Gene #54: '11Q LOSS MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	229	55	0.0 - 211.2 (14.5)
11Q LOSS MUTATED	9	5	0.2 - 41.1 (15.0)
11Q LOSS WILD-TYPE	220	50	0.0 - 211.2 (14.5)

Figure S16. Get High-res Image Gene #54: '11Q LOSS MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'17P LOSS MUTATION STATUS' versus 'Time to Death'

P value = 0.000276 (logrank test), Q value = 0.11

Table S17. Gene #62: '17P LOSS MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	229	55	0.0 - 211.2 (14.5)
17P LOSS MUTATED	10	4	0.1 - 23.7 (12.3)
17P LOSS WILD-TYPE	219	51	0.0 - 211.2 (14.5)

Figure S17. Get High-res Image Gene #62: '17P LOSS MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'17P LOSS MUTATION STATUS' versus 'AGE'

P value = 0.000572 (t-test), Q value = 0.23

Table S18. Gene #62: '17P LOSS MUTATION STATUS' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	229	42.8 (13.4)
17P LOSS MUTATED	10	54.7 (7.9)
17P LOSS WILD-TYPE	219	42.2 (13.3)

Figure S18. Get High-res Image Gene #62: '17P LOSS MUTATION STATUS' versus Clinical Feature #2: 'AGE'

'19Q LOSS MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 6.56e-14 (Fisher's exact test), Q value = 2.8e-11

Table S19. Gene #67: '19Q LOSS MUTATION STATUS' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	71	64	93
19Q LOSS MUTATED	10	14	63
19Q LOSS WILD-TYPE	61	50	30

Figure S19. Get High-res Image Gene #67: '19Q LOSS MUTATION STATUS' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Clinical data file = LGG-TP.clin.merged.picked.txt
Number of patients = 229
Number of significantly arm-level cnvs = 71
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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