Correlation between copy number variation genes (focal events) 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 variation genes (focal events) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1SB440T

Overview

Introduction

This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.

Summary

Testing the association between copy number variation 48 focal events and 6 clinical features across 229 patients, 14 significant findings detected with Q value < 0.25.

AMP PEAK 2(1Q32.1) MUTATION ANALYSIS cnv correlated to 'AGE'.
AMP PEAK 4(3Q26.32) MUTATION ANALYSIS cnv correlated to 'Time to Death'.
AMP PEAK 6(7P11.2) MUTATION ANALYSIS cnv correlated to 'AGE'.
AMP PEAK 7(7Q32.3) MUTATION ANALYSIS cnv correlated to 'AGE'.
AMP PEAK 9(10P15.3) MUTATION ANALYSIS cnv correlated to 'AGE'.
AMP PEAK 13(12Q14.1) MUTATION ANALYSIS cnv correlated to 'Time to Death'.
AMP PEAK 18(19Q13.2) MUTATION ANALYSIS cnv correlated to 'Time to Death' and 'AGE'.
DEL PEAK 1(1P36.31) MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.
DEL PEAK 2(1P32.3) MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.
DEL PEAK 12(9P21.3) MUTATION ANALYSIS cnv correlated to 'Time to Death' and 'AGE'.
DEL PEAK 13(10Q26.3) MUTATION ANALYSIS cnv correlated to 'Time to Death'.
DEL PEAK 25(19Q13.42) 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 48 focal events and 6 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 14 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
AMP PEAK 18(19Q13 2) MUTATION ANALYSIS	16 (7%)	213	1e-05 (0.00285)	2.3e-05 (0.0065)	1 (1.00)	0.543 (1.00)	0.546 (1.00)	0.429 (1.00)
DEL PEAK 12(9P21 3) MUTATION ANALYSIS	83 (36%)	146	5.18e-06 (0.00148)	6.22e-05 (0.0173)	0.784 (1.00)	0.317 (1.00)	0.0225 (1.00)	0.0241 (1.00)
AMP PEAK 2(1Q32 1) MUTATION ANALYSIS	24 (10%)	205	0.0751 (1.00)	3.9e-05 (0.011)	0.387 (1.00)	0.109 (1.00)	0.119 (1.00)	0.513 (1.00)
AMP PEAK 4(3Q26 32) MUTATION ANALYSIS	11 (5%)	218	0.000178 (0.0492)	0.295 (1.00)	0.758 (1.00)	0.535 (1.00)	0.0488 (1.00)	0.116 (1.00)
AMP PEAK 6(7P11 2) MUTATION ANALYSIS	60 (26%)	169	0.00208 (0.566)	0.000161 (0.0447)	0.0698 (1.00)	0.402 (1.00)	0.0339 (1.00)	0.759 (1.00)
AMP PEAK 7(7Q32 3) MUTATION ANALYSIS	82 (36%)	147	0.124 (1.00)	3.39e-05 (0.00955)	0.0519 (1.00)	0.927 (1.00)	0.196 (1.00)	0.673 (1.00)
AMP PEAK 9(10P15 3) MUTATION ANALYSIS	34 (15%)	195	0.435 (1.00)	0.000429 (0.118)	0.266 (1.00)	0.716 (1.00)	0.0075 (1.00)	0.186 (1.00)
AMP PEAK 13(12Q14 1) MUTATION ANALYSIS	15 (7%)	214	4.94e-05 (0.0138)	0.101 (1.00)	0.284 (1.00)	0.356 (1.00)	0.164 (1.00)	1 (1.00)
DEL PEAK 1(1P36 31) MUTATION ANALYSIS	86 (38%)	143	0.776 (1.00)	0.00122 (0.333)	0.494 (1.00)	0.499 (1.00)	1.19e-13 (3.4e-11)	0.125 (1.00)
DEL PEAK 2(1P32 3) MUTATION ANALYSIS	81 (35%)	148	0.106 (1.00)	0.00212 (0.575)	0.677 (1.00)	0.576 (1.00)	9.71e-15 (2.8e-12)	0.0159 (1.00)
DEL PEAK 13(10Q26 3) MUTATION ANALYSIS	70 (31%)	159	4.06e-05 (0.0114)	0.00433 (1.00)	0.0606 (1.00)	0.808 (1.00)	0.00687 (1.00)	0.884 (1.00)
DEL PEAK 25(19Q13 42) MUTATION ANALYSIS	118 (52%)	111	0.0362 (1.00)	0.673 (1.00)	0.509 (1.00)	0.844 (1.00)	2.5e-08 (7.15e-06)	0.893 (1.00)
AMP PEAK 1(1Q22) MUTATION ANALYSIS	22 (10%)	207	0.127 (1.00)	0.00637 (1.00)	0.178 (1.00)	0.877 (1.00)	0.61 (1.00)	0.647 (1.00)
AMP PEAK 3(3P24 3) MUTATION ANALYSIS	12 (5%)	217	0.124 (1.00)	0.966 (1.00)	0.555 (1.00)	0.439 (1.00)	0.361 (1.00)	0.546 (1.00)
AMP PEAK 5(4Q12) MUTATION ANALYSIS	10 (4%)	219	0.439 (1.00)	0.557 (1.00)	0.755 (1.00)	0.346 (1.00)	0.0488 (1.00)	1 (1.00)
AMP PEAK 8(8Q24 12) MUTATION ANALYSIS	46 (20%)	183	0.717 (1.00)	0.419 (1.00)	0.0964 (1.00)	0.557 (1.00)	0.0167 (1.00)	0.613 (1.00)
AMP PEAK 10(11Q23 3) MUTATION ANALYSIS	39 (17%)	190	0.997 (1.00)	0.275 (1.00)	0.861 (1.00)	0.717 (1.00)	0.794 (1.00)	1 (1.00)
AMP PEAK 11(12P13 32) MUTATION ANALYSIS	36 (16%)	193	0.57 (1.00)	0.0444 (1.00)	0.149 (1.00)	0.557 (1.00)	0.352 (1.00)	0.193 (1.00)
AMP PEAK 12(12P12 1) MUTATION ANALYSIS	22 (10%)	207	0.644 (1.00)	0.133 (1.00)	0.114 (1.00)	0.483 (1.00)	0.324 (1.00)	0.168 (1.00)
AMP PEAK 14(13Q33 3) MUTATION ANALYSIS	8 (3%)	221	0.236 (1.00)	0.904 (1.00)	0.304 (1.00)	0.106 (1.00)	0.443 (1.00)	0.715 (1.00)
AMP PEAK 15(17Q25 1) MUTATION ANALYSIS	14 (6%)	215	0.00368 (0.985)	0.25 (1.00)	1 (1.00)	0.792 (1.00)	0.648 (1.00)	0.411 (1.00)
AMP PEAK 16(18Q23) MUTATION ANALYSIS	8 (3%)	221	0.035 (1.00)	0.457 (1.00)	1 (1.00)	0.0763 (1.00)	0.243 (1.00)	0.269 (1.00)
AMP PEAK 17(19P13 3) MUTATION ANALYSIS	53 (23%)	176	0.736 (1.00)	0.094 (1.00)	0.639 (1.00)	0.268 (1.00)	0.0121 (1.00)	1 (1.00)
AMP PEAK 19(XP22 33) MUTATION ANALYSIS	14 (6%)	215	0.548 (1.00)	0.792 (1.00)	1 (1.00)	0.555 (1.00)	0.00443 (1.00)	0.17 (1.00)
AMP PEAK 20(XP11 22) MUTATION ANALYSIS	31 (14%)	198	0.722 (1.00)	0.919 (1.00)	0.121 (1.00)	0.315 (1.00)	0.0123 (1.00)	0.554 (1.00)
DEL PEAK 3(1Q43) MUTATION ANALYSIS	13 (6%)	216	0.626 (1.00)	0.984 (1.00)	0.255 (1.00)	0.802 (1.00)	0.491 (1.00)	1 (1.00)
DEL PEAK 4(2P25 3) MUTATION ANALYSIS	18 (8%)	211	0.333 (1.00)	0.353 (1.00)	0.806 (1.00)	0.803 (1.00)	0.0386 (1.00)	0.626 (1.00)
DEL PEAK 5(2Q37 1) MUTATION ANALYSIS	29 (13%)	200	0.907 (1.00)	0.0252 (1.00)	0.43 (1.00)	0.0825 (1.00)	0.142 (1.00)	0.84 (1.00)
DEL PEAK 6(2Q37 3) MUTATION ANALYSIS	32 (14%)	197	0.793 (1.00)	0.0699 (1.00)	1 (1.00)	0.604 (1.00)	0.167 (1.00)	0.697 (1.00)
DEL PEAK 7(3P21 1) MUTATION ANALYSIS	20 (9%)	209	0.138 (1.00)	0.0269 (1.00)	0.482 (1.00)	0.494 (1.00)	0.369 (1.00)	0.0568 (1.00)
DEL PEAK 8(4Q35 2) MUTATION ANALYSIS	66 (29%)	163	0.668 (1.00)	0.698 (1.00)	0.24 (1.00)	0.513 (1.00)	0.216 (1.00)	0.236 (1.00)
DEL PEAK 9(5Q35 2) MUTATION ANALYSIS	28 (12%)	201	0.0472 (1.00)	0.525 (1.00)	0.417 (1.00)	0.236 (1.00)	0.142 (1.00)	0.00641 (1.00)
DEL PEAK 10(6P25 3) MUTATION ANALYSIS	21 (9%)	208	0.00227 (0.612)	0.524 (1.00)	0.495 (1.00)	0.326 (1.00)	0.00728 (1.00)	1 (1.00)
DEL PEAK 11(6Q24 3) MUTATION ANALYSIS	36 (16%)	193	0.0287 (1.00)	0.243 (1.00)	0.201 (1.00)	0.452 (1.00)	0.0133 (1.00)	0.578 (1.00)
DEL PEAK 14(11P15 5) MUTATION ANALYSIS	46 (20%)	183	0.252 (1.00)	0.0617 (1.00)	0.14 (1.00)	0.657 (1.00)	0.028 (1.00)	0.866 (1.00)
DEL PEAK 15(11Q25) MUTATION ANALYSIS	15 (7%)	214	0.00925 (1.00)	0.991 (1.00)	0.593 (1.00)	0.535 (1.00)	0.367 (1.00)	1 (1.00)
DEL PEAK 16(12Q12) MUTATION ANALYSIS	28 (12%)	201	0.824 (1.00)	0.605 (1.00)	0.842 (1.00)	0.802 (1.00)	0.183 (1.00)	1 (1.00)
DEL PEAK 17(13Q14 2) MUTATION ANALYSIS	67 (29%)	162	0.435 (1.00)	0.874 (1.00)	0.662 (1.00)	0.0894 (1.00)	0.133 (1.00)	0.182 (1.00)
DEL PEAK 18(13Q21 2) MUTATION ANALYSIS	69 (30%)	160	0.301 (1.00)	0.908 (1.00)	0.665 (1.00)	0.0894 (1.00)	0.128 (1.00)	0.302 (1.00)
DEL PEAK 19(13Q22 1) MUTATION ANALYSIS	68 (30%)	161	0.305 (1.00)	0.794 (1.00)	0.772 (1.00)	0.13 (1.00)	0.198 (1.00)	0.237 (1.00)
DEL PEAK 20(13Q34) MUTATION ANALYSIS	52 (23%)	177	0.184 (1.00)	0.51 (1.00)	0.635 (1.00)	0.471 (1.00)	0.796 (1.00)	0.631 (1.00)
DEL PEAK 21(14Q24 3) MUTATION ANALYSIS	53 (23%)	176	0.00297 (0.798)	0.171 (1.00)	0.0581 (1.00)	0.868 (1.00)	0.108 (1.00)	0.523 (1.00)
DEL PEAK 22(17Q25 3) MUTATION ANALYSIS	14 (6%)	215	0.849 (1.00)	0.203 (1.00)	1 (1.00)	0.326 (1.00)	0.832 (1.00)	0.784 (1.00)
DEL PEAK 23(18P11 32) MUTATION ANALYSIS	33 (14%)	196	0.994 (1.00)	0.909 (1.00)	0.0894 (1.00)	0.315 (1.00)	0.791 (1.00)	0.128 (1.00)
DEL PEAK 24(18Q23) MUTATION ANALYSIS	36 (16%)	193	0.455 (1.00)	0.355 (1.00)	1 (1.00)	0.948 (1.00)	0.803 (1.00)	0.578 (1.00)
DEL PEAK 26(22Q13 31) MUTATION ANALYSIS	33 (14%)	196	0.0914 (1.00)	0.142 (1.00)	0.257 (1.00)	0.541 (1.00)	0.00118 (0.323)	0.704 (1.00)
DEL PEAK 27(XP22 2) MUTATION ANALYSIS	47 (21%)	182	0.404 (1.00)	0.991 (1.00)	0.192 (1.00)	0.456 (1.00)	1 (1.00)	0.738 (1.00)
DEL PEAK 28(XQ21 1) MUTATION ANALYSIS	31 (14%)	198	0.386 (1.00)	0.146 (1.00)	0.44 (1.00)	0.895 (1.00)	0.23 (1.00)	0.844 (1.00)

'AMP PEAK 2(1Q32.1) MUTATION STATUS' versus 'AGE'

P value = 3.9e-05 (t-test), Q value = 0.011

Table S1. Gene #2: 'AMP PEAK 2(1Q32.1) MUTATION STATUS' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	229	42.8 (13.4)
AMP PEAK 2(1Q32.1) MUTATED	24	53.3 (11.2)
AMP PEAK 2(1Q32.1) WILD-TYPE	205	41.5 (13.1)

Figure S1. Get High-res Image Gene #2: 'AMP PEAK 2(1Q32.1) MUTATION STATUS' versus Clinical Feature #2: 'AGE'

'AMP PEAK 4(3Q26.32) MUTATION STATUS' versus 'Time to Death'

P value = 0.000178 (logrank test), Q value = 0.049

Table S2. Gene #4: 'AMP PEAK 4(3Q26.32) MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	229	55	0.0 - 211.2 (14.5)
AMP PEAK 4(3Q26.32) MUTATED	11	5	0.2 - 41.1 (8.8)
AMP PEAK 4(3Q26.32) WILD-TYPE	218	50	0.0 - 211.2 (14.7)

Figure S2. Get High-res Image Gene #4: 'AMP PEAK 4(3Q26.32) MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'AMP PEAK 6(7P11.2) MUTATION STATUS' versus 'AGE'

P value = 0.000161 (t-test), Q value = 0.045

Table S3. Gene #6: 'AMP PEAK 6(7P11.2) MUTATION STATUS' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	229	42.8 (13.4)
AMP PEAK 6(7P11.2) MUTATED	60	48.5 (13.3)
AMP PEAK 6(7P11.2) WILD-TYPE	169	40.7 (12.8)

Figure S3. Get High-res Image Gene #6: 'AMP PEAK 6(7P11.2) MUTATION STATUS' versus Clinical Feature #2: 'AGE'

'AMP PEAK 7(7Q32.3) MUTATION STATUS' versus 'AGE'

P value = 3.39e-05 (t-test), Q value = 0.0095

Table S4. Gene #7: 'AMP PEAK 7(7Q32.3) MUTATION STATUS' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	229	42.8 (13.4)
AMP PEAK 7(7Q32.3) MUTATED	82	47.6 (13.0)
AMP PEAK 7(7Q32.3) WILD-TYPE	147	40.0 (12.8)

Figure S4. Get High-res Image Gene #7: 'AMP PEAK 7(7Q32.3) MUTATION STATUS' versus Clinical Feature #2: 'AGE'

'AMP PEAK 9(10P15.3) MUTATION STATUS' versus 'AGE'

P value = 0.000429 (t-test), Q value = 0.12

Table S5. Gene #9: 'AMP PEAK 9(10P15.3) MUTATION STATUS' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	229	42.8 (13.4)
AMP PEAK 9(10P15.3) MUTATED	34	36.3 (10.4)
AMP PEAK 9(10P15.3) WILD-TYPE	195	43.9 (13.5)

Figure S5. Get High-res Image Gene #9: 'AMP PEAK 9(10P15.3) MUTATION STATUS' versus Clinical Feature #2: 'AGE'

'AMP PEAK 13(12Q14.1) MUTATION STATUS' versus 'Time to Death'

P value = 4.94e-05 (logrank test), Q value = 0.014

Table S6. Gene #13: 'AMP PEAK 13(12Q14.1) MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	229	55	0.0 - 211.2 (14.5)
AMP PEAK 13(12Q14.1) MUTATED	15	9	1.2 - 80.0 (12.4)
AMP PEAK 13(12Q14.1) WILD-TYPE	214	46	0.0 - 211.2 (14.5)

Figure S6. Get High-res Image Gene #13: 'AMP PEAK 13(12Q14.1) MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'AMP PEAK 18(19Q13.2) MUTATION STATUS' versus 'Time to Death'

P value = 1e-05 (logrank test), Q value = 0.0028

Table S7. Gene #18: 'AMP PEAK 18(19Q13.2) MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	229	55	0.0 - 211.2 (14.5)
AMP PEAK 18(19Q13.2) MUTATED	16	7	0.0 - 43.9 (12.9)
AMP PEAK 18(19Q13.2) WILD-TYPE	213	48	0.1 - 211.2 (14.5)

Figure S7. Get High-res Image Gene #18: 'AMP PEAK 18(19Q13.2) MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'AMP PEAK 18(19Q13.2) MUTATION STATUS' versus 'AGE'

P value = 2.3e-05 (t-test), Q value = 0.0065

Table S8. Gene #18: 'AMP PEAK 18(19Q13.2) MUTATION STATUS' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	229	42.8 (13.4)
AMP PEAK 18(19Q13.2) MUTATED	16	53.4 (7.8)
AMP PEAK 18(19Q13.2) WILD-TYPE	213	42.0 (13.4)

Figure S8. Get High-res Image Gene #18: 'AMP PEAK 18(19Q13.2) MUTATION STATUS' versus Clinical Feature #2: 'AGE'

'DEL PEAK 1(1P36.31) MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 1.19e-13 (Fisher's exact test), Q value = 3.4e-11

Table S9. Gene #21: 'DEL PEAK 1(1P36.31) MUTATION STATUS' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	71	64	93
DEL PEAK 1(1P36.31) MUTATED	9	15	62
DEL PEAK 1(1P36.31) WILD-TYPE	62	49	31

Figure S9. Get High-res Image Gene #21: 'DEL PEAK 1(1P36.31) MUTATION STATUS' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'DEL PEAK 2(1P32.3) MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 9.71e-15 (Fisher's exact test), Q value = 2.8e-12

Table S10. Gene #22: 'DEL PEAK 2(1P32.3) MUTATION STATUS' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	71	64	93
DEL PEAK 2(1P32.3) MUTATED	8	12	61
DEL PEAK 2(1P32.3) WILD-TYPE	63	52	32

Figure S10. Get High-res Image Gene #22: 'DEL PEAK 2(1P32.3) MUTATION STATUS' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'DEL PEAK 12(9P21.3) MUTATION STATUS' versus 'Time to Death'

P value = 5.18e-06 (logrank test), Q value = 0.0015

Table S11. Gene #32: 'DEL PEAK 12(9P21.3) MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	229	55	0.0 - 211.2 (14.5)
DEL PEAK 12(9P21.3) MUTATED	83	29	0.1 - 117.4 (16.2)
DEL PEAK 12(9P21.3) WILD-TYPE	146	26	0.0 - 211.2 (14.3)

Figure S11. Get High-res Image Gene #32: 'DEL PEAK 12(9P21.3) MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'DEL PEAK 12(9P21.3) MUTATION STATUS' versus 'AGE'

P value = 6.22e-05 (t-test), Q value = 0.017

Table S12. Gene #32: 'DEL PEAK 12(9P21.3) MUTATION STATUS' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	229	42.8 (13.4)
DEL PEAK 12(9P21.3) MUTATED	83	47.4 (12.9)
DEL PEAK 12(9P21.3) WILD-TYPE	146	40.1 (12.9)

Figure S12. Get High-res Image Gene #32: 'DEL PEAK 12(9P21.3) MUTATION STATUS' versus Clinical Feature #2: 'AGE'

'DEL PEAK 13(10Q26.3) MUTATION STATUS' versus 'Time to Death'

P value = 4.06e-05 (logrank test), Q value = 0.011

Table S13. Gene #33: 'DEL PEAK 13(10Q26.3) MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	229	55	0.0 - 211.2 (14.5)
DEL PEAK 13(10Q26.3) MUTATED	70	32	0.1 - 156.2 (15.3)
DEL PEAK 13(10Q26.3) WILD-TYPE	159	23	0.0 - 211.2 (14.4)

Figure S13. Get High-res Image Gene #33: 'DEL PEAK 13(10Q26.3) MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'DEL PEAK 25(19Q13.42) MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 2.5e-08 (Fisher's exact test), Q value = 7.2e-06

Table S14. Gene #45: 'DEL PEAK 25(19Q13.42) MUTATION STATUS' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	71	64	93
DEL PEAK 25(19Q13.42) MUTATED	22	26	69
DEL PEAK 25(19Q13.42) WILD-TYPE	49	38	24

Figure S14. Get High-res Image Gene #45: 'DEL PEAK 25(19Q13.42) 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 focal cnvs = 48
Number of selected clinical features = 6
Exclude genes 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)

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