Correlation between copy number variation genes (focal events) 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 variation genes (focal events) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1R2101D

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 359 patients, 30 significant findings detected with Q value < 0.25.

amp_1q32.1 cnv correlated to 'AGE'.
amp_1q43 cnv correlated to 'AGE'.
amp_7p11.2 cnv correlated to 'Time to Death' and 'AGE'.
amp_7q31.2 cnv correlated to 'AGE'.
amp_7q32.3 cnv correlated to 'AGE'.
amp_8q24.13 cnv correlated to 'HISTOLOGICAL.TYPE'.
amp_10p15.3 cnv correlated to 'AGE' and 'HISTOLOGICAL.TYPE'.
amp_12q14.1 cnv correlated to 'Time to Death' and 'AGE'.
amp_19p13.3 cnv correlated to 'HISTOLOGICAL.TYPE'.
amp_19p13.2 cnv correlated to 'HISTOLOGICAL.TYPE'.
del_1p36.23 cnv correlated to 'AGE' and 'HISTOLOGICAL.TYPE'.
del_1p32.3 cnv correlated to 'AGE' and 'HISTOLOGICAL.TYPE'.
del_5q34 cnv correlated to 'HISTOLOGICAL.TYPE'.
del_6p25.3 cnv correlated to 'Time to Death'.
del_6q24.3 cnv correlated to 'HISTOLOGICAL.TYPE'.
del_9p23 cnv correlated to 'Time to Death'.
del_9p21.3 cnv correlated to 'Time to Death' and 'AGE'.
del_10q26.3 cnv correlated to 'Time to Death', 'AGE', and 'HISTOLOGICAL.TYPE'.
del_11p15.5 cnv correlated to 'HISTOLOGICAL.TYPE'.
del_12p13.1 cnv correlated to 'Time to Death'.
del_14q24.3 cnv correlated to 'Time to Death'.
del_19q13.42 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, 30 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
del 10q26 3	104 (29%)	255	1.71e-08 (4.86e-06)	2.45e-05 (0.00664)	0.0622 (1.00)	0.132 (1.00)	0.00053 (0.138)	1 (1.00)
amp 7p11 2	91 (25%)	268	2.71e-06 (0.00076)	2.73e-07 (7.69e-05)	0.225 (1.00)	0.0208 (1.00)	0.0205 (1.00)	0.486 (1.00)
amp 10p15 3	46 (13%)	313	0.862 (1.00)	4.04e-06 (0.00111)	0.115 (1.00)	0.25 (1.00)	0.000314 (0.0829)	0.0267 (1.00)
amp 12q14 1	26 (7%)	333	2.57e-08 (7.26e-06)	0.000742 (0.192)	0.421 (1.00)	0.44 (1.00)	0.0459 (1.00)	0.346 (1.00)
del 1p36 23	152 (42%)	207	0.459 (1.00)	2.96e-06 (0.000826)	0.393 (1.00)	0.592 (1.00)	1.45e-24 (4.17e-22)	0.0356 (1.00)
del 1p32 3	140 (39%)	219	0.029 (1.00)	4.84e-05 (0.0131)	0.588 (1.00)	0.859 (1.00)	1.96e-29 (5.65e-27)	0.00383 (0.95)
del 9p21 3	118 (33%)	241	1.84e-10 (5.25e-08)	3.79e-06 (0.00105)	0.91 (1.00)	0.0114 (1.00)	0.00171 (0.437)	0.0063 (1.00)
amp 1q32 1	31 (9%)	328	0.00255 (0.643)	7.76e-07 (0.000218)	0.851 (1.00)	0.156 (1.00)	0.229 (1.00)	0.383 (1.00)
amp 1q43	22 (6%)	337	0.00211 (0.536)	1.36e-05 (0.0037)	0.826 (1.00)	0.125 (1.00)	0.314 (1.00)	0.206 (1.00)
amp 7q31 2	125 (35%)	234	0.00276 (0.693)	4.82e-06 (0.00132)	0.0969 (1.00)	0.112 (1.00)	0.0354 (1.00)	0.61 (1.00)
amp 7q32 3	132 (37%)	227	0.0043 (1.00)	3.17e-06 (0.000881)	0.0789 (1.00)	0.17 (1.00)	0.0351 (1.00)	0.613 (1.00)
amp 8q24 13	71 (20%)	288	0.821 (1.00)	0.2 (1.00)	0.145 (1.00)	0.14 (1.00)	0.000165 (0.0439)	0.879 (1.00)
amp 19p13 3	92 (26%)	267	0.91 (1.00)	0.0235 (1.00)	0.809 (1.00)	0.639 (1.00)	2.01e-05 (0.00547)	0.676 (1.00)
amp 19p13 2	86 (24%)	273	0.714 (1.00)	0.00447 (1.00)	0.389 (1.00)	0.472 (1.00)	3.55e-06 (0.000983)	1 (1.00)
del 5q34	47 (13%)	312	0.0162 (1.00)	0.449 (1.00)	1 (1.00)	0.944 (1.00)	0.000553 (0.144)	0.146 (1.00)
del 6p25 3	35 (10%)	324	0.000141 (0.0376)	0.326 (1.00)	0.725 (1.00)	0.144 (1.00)	0.0807 (1.00)	0.84 (1.00)
del 6q24 3	55 (15%)	304	0.00245 (0.62)	0.512 (1.00)	0.464 (1.00)	0.43 (1.00)	9.3e-05 (0.0249)	0.308 (1.00)
del 9p23	98 (27%)	261	8.6e-05 (0.0231)	0.00969 (1.00)	0.813 (1.00)	0.157 (1.00)	0.00997 (1.00)	0.00929 (1.00)
del 11p15 5	72 (20%)	287	0.253 (1.00)	0.0143 (1.00)	0.0242 (1.00)	0.532 (1.00)	0.000504 (0.132)	0.542 (1.00)
del 12p13 1	26 (7%)	333	0.000396 (0.104)	0.847 (1.00)	0.541 (1.00)	0.393 (1.00)	0.0773 (1.00)	0.241 (1.00)
del 14q24 3	82 (23%)	277	0.000266 (0.0705)	0.0444 (1.00)	0.13 (1.00)	0.536 (1.00)	0.107 (1.00)	0.663 (1.00)
del 19q13 42	191 (53%)	168	0.0177 (1.00)	0.305 (1.00)	1 (1.00)	0.632 (1.00)	3.05e-17 (8.73e-15)	0.903 (1.00)
amp 2p24 3	11 (3%)	348	0.3 (1.00)	0.532 (1.00)	0.76 (1.00)	0.585 (1.00)	0.247 (1.00)	0.737 (1.00)
amp 3q26 32	16 (4%)	343	0.0054 (1.00)	0.0942 (1.00)	0.801 (1.00)	0.533 (1.00)	0.0151 (1.00)	0.241 (1.00)
amp 4q12	17 (5%)	342	0.0185 (1.00)	0.21 (1.00)	1 (1.00)	0.383 (1.00)	0.0419 (1.00)	1 (1.00)
amp 11q23 3	61 (17%)	298	0.698 (1.00)	0.44 (1.00)	0.204 (1.00)	0.807 (1.00)	0.892 (1.00)	1 (1.00)
amp 12p13 32	53 (15%)	306	0.321 (1.00)	0.167 (1.00)	0.036 (1.00)	0.377 (1.00)	0.133 (1.00)	0.12 (1.00)
amp 13q34	16 (4%)	343	0.398 (1.00)	0.799 (1.00)	1 (1.00)	0.421 (1.00)	0.769 (1.00)	1 (1.00)
amp 15q26 3	13 (4%)	346	0.00123 (0.315)	0.761 (1.00)	1 (1.00)	0.148 (1.00)	0.105 (1.00)	0.743 (1.00)
amp 17q25 1	27 (8%)	332	0.00163 (0.416)	0.165 (1.00)	0.689 (1.00)	0.675 (1.00)	0.153 (1.00)	1 (1.00)
amp xp11 22	35 (10%)	324	0.82 (1.00)	0.335 (1.00)	0.859 (1.00)	0.952 (1.00)	0.0104 (1.00)	0.545 (1.00)
del 1q43	18 (5%)	341	0.719 (1.00)	0.922 (1.00)	0.228 (1.00)	0.23 (1.00)	0.21 (1.00)	0.781 (1.00)
del 2q37 3	52 (14%)	307	0.8 (1.00)	0.0935 (1.00)	0.293 (1.00)	0.778 (1.00)	0.019 (1.00)	0.489 (1.00)
del 3p21 1	29 (8%)	330	0.0391 (1.00)	0.588 (1.00)	0.439 (1.00)	0.0152 (1.00)	0.369 (1.00)	0.0421 (1.00)
del 3q29	29 (8%)	330	0.0189 (1.00)	0.854 (1.00)	0.245 (1.00)	0.274 (1.00)	0.141 (1.00)	0.5 (1.00)
del 4q34 3	101 (28%)	258	0.573 (1.00)	0.226 (1.00)	0.638 (1.00)	0.774 (1.00)	0.862 (1.00)	0.281 (1.00)
del 5p15 33	34 (9%)	325	0.992 (1.00)	0.132 (1.00)	0.371 (1.00)	0.103 (1.00)	0.00468 (1.00)	0.0109 (1.00)
del 7p22 3	17 (5%)	342	0.774 (1.00)	0.467 (1.00)	0.458 (1.00)	0.582 (1.00)	0.295 (1.00)	0.773 (1.00)
del 8q24 3	20 (6%)	339	0.407 (1.00)	0.728 (1.00)	1 (1.00)	0.981 (1.00)	0.107 (1.00)	0.597 (1.00)
del 12q12	46 (13%)	313	0.682 (1.00)	0.658 (1.00)	0.429 (1.00)	0.638 (1.00)	0.00103 (0.266)	0.855 (1.00)
del 13q14 2	100 (28%)	259	0.0291 (1.00)	0.752 (1.00)	0.408 (1.00)	0.0176 (1.00)	0.261 (1.00)	0.102 (1.00)
del 13q14 2	102 (28%)	257	0.0411 (1.00)	0.787 (1.00)	0.411 (1.00)	0.0187 (1.00)	0.195 (1.00)	0.137 (1.00)
del 13q34	76 (21%)	283	0.0358 (1.00)	0.868 (1.00)	0.698 (1.00)	0.358 (1.00)	0.907 (1.00)	0.232 (1.00)
del 18q23	57 (16%)	302	0.916 (1.00)	0.0721 (1.00)	0.248 (1.00)	0.524 (1.00)	0.695 (1.00)	0.741 (1.00)
del 22q13 31	52 (14%)	307	0.00404 (0.999)	0.00744 (1.00)	0.881 (1.00)	0.0364 (1.00)	0.0034 (0.849)	0.729 (1.00)
del 22q13 31	51 (14%)	308	0.00366 (0.912)	0.00953 (1.00)	0.762 (1.00)	0.0343 (1.00)	0.006 (1.00)	0.604 (1.00)
del xp21 1	69 (19%)	290	0.15 (1.00)	0.553 (1.00)	0.107 (1.00)	0.141 (1.00)	0.956 (1.00)	0.877 (1.00)
del xq21 1	49 (14%)	310	0.199 (1.00)	0.0347 (1.00)	0.648 (1.00)	0.643 (1.00)	0.345 (1.00)	1 (1.00)

'amp_1q32.1' versus 'AGE'

P value = 7.76e-07 (t-test), Q value = 0.00022

Table S1. Gene #1: 'amp_1q32.1' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	359	43.6 (13.5)
AMP PEAK 1(1Q32.1) MUTATED	31	55.5 (11.6)
AMP PEAK 1(1Q32.1) WILD-TYPE	328	42.5 (13.1)

Figure S1. Get High-res Image Gene #1: 'amp_1q32.1' versus Clinical Feature #2: 'AGE'

'amp_1q43' versus 'AGE'

P value = 1.36e-05 (t-test), Q value = 0.0037

Table S2. Gene #2: 'amp_1q43' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	359	43.6 (13.5)
AMP PEAK 2(1Q43) MUTATED	22	55.8 (10.8)
AMP PEAK 2(1Q43) WILD-TYPE	337	42.8 (13.3)

Figure S2. Get High-res Image Gene #2: 'amp_1q43' versus Clinical Feature #2: 'AGE'

'amp_7p11.2' versus 'Time to Death'

P value = 2.71e-06 (logrank test), Q value = 0.00076

Table S3. Gene #6: 'amp_7p11.2' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	356	68	0.0 - 211.2 (14.8)
AMP PEAK 6(7P11.2) MUTATED	90	33	0.1 - 211.2 (13.1)
AMP PEAK 6(7P11.2) WILD-TYPE	266	35	0.0 - 182.3 (15.1)

Figure S3. Get High-res Image Gene #6: 'amp_7p11.2' versus Clinical Feature #1: 'Time to Death'

'amp_7p11.2' versus 'AGE'

P value = 2.73e-07 (t-test), Q value = 7.7e-05

Table S4. Gene #6: 'amp_7p11.2' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	359	43.6 (13.5)
AMP PEAK 6(7P11.2) MUTATED	91	50.2 (13.9)
AMP PEAK 6(7P11.2) WILD-TYPE	268	41.4 (12.6)

Figure S4. Get High-res Image Gene #6: 'amp_7p11.2' versus Clinical Feature #2: 'AGE'

'amp_7q31.2' versus 'AGE'

P value = 4.82e-06 (t-test), Q value = 0.0013

Table S5. Gene #7: 'amp_7q31.2' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	359	43.6 (13.5)
AMP PEAK 7(7Q31.2) MUTATED	125	48.1 (13.7)
AMP PEAK 7(7Q31.2) WILD-TYPE	234	41.2 (12.8)

Figure S5. Get High-res Image Gene #7: 'amp_7q31.2' versus Clinical Feature #2: 'AGE'

'amp_7q32.3' versus 'AGE'

P value = 3.17e-06 (t-test), Q value = 0.00088

Table S6. Gene #8: 'amp_7q32.3' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	359	43.6 (13.5)
AMP PEAK 8(7Q32.3) MUTATED	132	48.0 (13.5)
AMP PEAK 8(7Q32.3) WILD-TYPE	227	41.1 (12.8)

Figure S6. Get High-res Image Gene #8: 'amp_7q32.3' versus Clinical Feature #2: 'AGE'

'amp_8q24.13' versus 'HISTOLOGICAL.TYPE'

P value = 0.000165 (Fisher's exact test), Q value = 0.044

Table S7. Gene #9: 'amp_8q24.13' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	123	99	137
AMP PEAK 9(8Q24.13) MUTATED	36	22	13
AMP PEAK 9(8Q24.13) WILD-TYPE	87	77	124

Figure S7. Get High-res Image Gene #9: 'amp_8q24.13' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'amp_10p15.3' versus 'AGE'

P value = 4.04e-06 (t-test), Q value = 0.0011

Table S8. Gene #10: 'amp_10p15.3' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	359	43.6 (13.5)
AMP PEAK 10(10P15.3) MUTATED	46	36.4 (9.9)
AMP PEAK 10(10P15.3) WILD-TYPE	313	44.7 (13.6)

Figure S8. Get High-res Image Gene #10: 'amp_10p15.3' versus Clinical Feature #2: 'AGE'

'amp_10p15.3' versus 'HISTOLOGICAL.TYPE'

P value = 0.000314 (Fisher's exact test), Q value = 0.083

Table S9. Gene #10: 'amp_10p15.3' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	123	99	137
AMP PEAK 10(10P15.3) MUTATED	22	18	6
AMP PEAK 10(10P15.3) WILD-TYPE	101	81	131

Figure S9. Get High-res Image Gene #10: 'amp_10p15.3' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'amp_12q14.1' versus 'Time to Death'

P value = 2.57e-08 (logrank test), Q value = 7.3e-06

Table S10. Gene #13: 'amp_12q14.1' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	356	68	0.0 - 211.2 (14.8)
AMP PEAK 13(12Q14.1) MUTATED	26	13	1.2 - 80.0 (11.9)
AMP PEAK 13(12Q14.1) WILD-TYPE	330	55	0.0 - 211.2 (15.0)

Figure S10. Get High-res Image Gene #13: 'amp_12q14.1' versus Clinical Feature #1: 'Time to Death'

'amp_12q14.1' versus 'AGE'

P value = 0.000742 (t-test), Q value = 0.19

Table S11. Gene #13: 'amp_12q14.1' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	359	43.6 (13.5)
AMP PEAK 13(12Q14.1) MUTATED	26	52.7 (12.7)
AMP PEAK 13(12Q14.1) WILD-TYPE	333	42.9 (13.3)

Figure S11. Get High-res Image Gene #13: 'amp_12q14.1' versus Clinical Feature #2: 'AGE'

'amp_19p13.3' versus 'HISTOLOGICAL.TYPE'

P value = 2.01e-05 (Fisher's exact test), Q value = 0.0055

Table S12. Gene #17: 'amp_19p13.3' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	123	99	137
AMP PEAK 17(19P13.3) MUTATED	16	24	52
AMP PEAK 17(19P13.3) WILD-TYPE	107	75	85

Figure S12. Get High-res Image Gene #17: 'amp_19p13.3' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'amp_19p13.2' versus 'HISTOLOGICAL.TYPE'

P value = 3.55e-06 (Fisher's exact test), Q value = 0.00098

Table S13. Gene #18: 'amp_19p13.2' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	123	99	137
AMP PEAK 18(19P13.2) MUTATED	15	19	52
AMP PEAK 18(19P13.2) WILD-TYPE	108	80	85

Figure S13. Get High-res Image Gene #18: 'amp_19p13.2' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'del_1p36.23' versus 'AGE'

P value = 2.96e-06 (t-test), Q value = 0.00083

Table S14. Gene #20: 'del_1p36.23' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	359	43.6 (13.5)
DEL PEAK 1(1P36.23) MUTATED	152	47.4 (13.0)
DEL PEAK 1(1P36.23) WILD-TYPE	207	40.8 (13.2)

Figure S14. Get High-res Image Gene #20: 'del_1p36.23' versus Clinical Feature #2: 'AGE'

'del_1p36.23' versus 'HISTOLOGICAL.TYPE'

P value = 1.45e-24 (Fisher's exact test), Q value = 4.2e-22

Table S15. Gene #20: 'del_1p36.23' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	123	99	137
DEL PEAK 1(1P36.23) MUTATED	15	36	101
DEL PEAK 1(1P36.23) WILD-TYPE	108	63	36

Figure S15. Get High-res Image Gene #20: 'del_1p36.23' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'del_1p32.3' versus 'AGE'

P value = 4.84e-05 (t-test), Q value = 0.013

Table S16. Gene #21: 'del_1p32.3' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	359	43.6 (13.5)
DEL PEAK 2(1P32.3) MUTATED	140	47.2 (13.1)
DEL PEAK 2(1P32.3) WILD-TYPE	219	41.3 (13.3)

Figure S16. Get High-res Image Gene #21: 'del_1p32.3' versus Clinical Feature #2: 'AGE'

'del_1p32.3' versus 'HISTOLOGICAL.TYPE'

P value = 1.96e-29 (Fisher's exact test), Q value = 5.7e-27

Table S17. Gene #21: 'del_1p32.3' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	123	99	137
DEL PEAK 2(1P32.3) MUTATED	9	31	100
DEL PEAK 2(1P32.3) WILD-TYPE	114	68	37

Figure S17. Get High-res Image Gene #21: 'del_1p32.3' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'del_5q34' versus 'HISTOLOGICAL.TYPE'

P value = 0.000553 (Fisher's exact test), Q value = 0.14

Table S18. Gene #28: 'del_5q34' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	123	99	137
DEL PEAK 9(5Q34) MUTATED	27	12	8
DEL PEAK 9(5Q34) WILD-TYPE	96	87	129

Figure S18. Get High-res Image Gene #28: 'del_5q34' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'del_6p25.3' versus 'Time to Death'

P value = 0.000141 (logrank test), Q value = 0.038

Table S19. Gene #29: 'del_6p25.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	356	68	0.0 - 211.2 (14.8)
DEL PEAK 10(6P25.3) MUTATED	34	12	0.2 - 94.5 (17.9)
DEL PEAK 10(6P25.3) WILD-TYPE	322	56	0.0 - 211.2 (14.5)

Figure S19. Get High-res Image Gene #29: 'del_6p25.3' versus Clinical Feature #1: 'Time to Death'

'del_6q24.3' versus 'HISTOLOGICAL.TYPE'

P value = 9.3e-05 (Fisher's exact test), Q value = 0.025

Table S20. Gene #30: 'del_6q24.3' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	123	99	137
DEL PEAK 11(6Q24.3) MUTATED	33	11	11
DEL PEAK 11(6Q24.3) WILD-TYPE	90	88	126

Figure S20. Get High-res Image Gene #30: 'del_6q24.3' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'del_9p23' versus 'Time to Death'

P value = 8.6e-05 (logrank test), Q value = 0.023

Table S21. Gene #33: 'del_9p23' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	356	68	0.0 - 211.2 (14.8)
DEL PEAK 14(9P23) MUTATED	97	28	0.1 - 117.4 (14.7)
DEL PEAK 14(9P23) WILD-TYPE	259	40	0.0 - 211.2 (15.0)

Figure S21. Get High-res Image Gene #33: 'del_9p23' versus Clinical Feature #1: 'Time to Death'

'del_9p21.3' versus 'Time to Death'

P value = 1.84e-10 (logrank test), Q value = 5.3e-08

Table S22. Gene #34: 'del_9p21.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	356	68	0.0 - 211.2 (14.8)
DEL PEAK 15(9P21.3) MUTATED	117	39	0.1 - 117.4 (14.2)
DEL PEAK 15(9P21.3) WILD-TYPE	239	29	0.0 - 211.2 (15.1)

Figure S22. Get High-res Image Gene #34: 'del_9p21.3' versus Clinical Feature #1: 'Time to Death'

'del_9p21.3' versus 'AGE'

P value = 3.79e-06 (t-test), Q value = 0.001

Table S23. Gene #34: 'del_9p21.3' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	359	43.6 (13.5)
DEL PEAK 15(9P21.3) MUTATED	118	48.4 (13.9)
DEL PEAK 15(9P21.3) WILD-TYPE	241	41.2 (12.6)

Figure S23. Get High-res Image Gene #34: 'del_9p21.3' versus Clinical Feature #2: 'AGE'

'del_10q26.3' versus 'Time to Death'

P value = 1.71e-08 (logrank test), Q value = 4.9e-06

Table S24. Gene #35: 'del_10q26.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	356	68	0.0 - 211.2 (14.8)
DEL PEAK 16(10Q26.3) MUTATED	103	41	0.1 - 156.2 (15.0)
DEL PEAK 16(10Q26.3) WILD-TYPE	253	27	0.0 - 211.2 (14.6)

Figure S24. Get High-res Image Gene #35: 'del_10q26.3' versus Clinical Feature #1: 'Time to Death'

'del_10q26.3' versus 'AGE'

P value = 2.45e-05 (t-test), Q value = 0.0066

Table S25. Gene #35: 'del_10q26.3' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	359	43.6 (13.5)
DEL PEAK 16(10Q26.3) MUTATED	104	48.5 (14.2)
DEL PEAK 16(10Q26.3) WILD-TYPE	255	41.6 (12.7)

Figure S25. Get High-res Image Gene #35: 'del_10q26.3' versus Clinical Feature #2: 'AGE'

'del_10q26.3' versus 'HISTOLOGICAL.TYPE'

P value = 0.00053 (Fisher's exact test), Q value = 0.14

Table S26. Gene #35: 'del_10q26.3' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	123	99	137
DEL PEAK 16(10Q26.3) MUTATED	51	26	27
DEL PEAK 16(10Q26.3) WILD-TYPE	72	73	110

Figure S26. Get High-res Image Gene #35: 'del_10q26.3' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'del_11p15.5' versus 'HISTOLOGICAL.TYPE'

P value = 0.000504 (Fisher's exact test), Q value = 0.13

Table S27. Gene #36: 'del_11p15.5' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	123	99	137
DEL PEAK 17(11P15.5) MUTATED	35	23	14
DEL PEAK 17(11P15.5) WILD-TYPE	88	76	123

Figure S27. Get High-res Image Gene #36: 'del_11p15.5' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'del_12p13.1' versus 'Time to Death'

P value = 0.000396 (logrank test), Q value = 0.1

Table S28. Gene #37: 'del_12p13.1' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	356	68	0.0 - 211.2 (14.8)
DEL PEAK 18(12P13.1) MUTATED	26	9	0.1 - 63.0 (10.9)
DEL PEAK 18(12P13.1) WILD-TYPE	330	59	0.0 - 211.2 (15.1)

Figure S28. Get High-res Image Gene #37: 'del_12p13.1' versus Clinical Feature #1: 'Time to Death'

'del_14q24.3' versus 'Time to Death'

P value = 0.000266 (logrank test), Q value = 0.071

Table S29. Gene #42: 'del_14q24.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	356	68	0.0 - 211.2 (14.8)
DEL PEAK 23(14Q24.3) MUTATED	81	28	0.2 - 130.8 (16.0)
DEL PEAK 23(14Q24.3) WILD-TYPE	275	40	0.0 - 211.2 (14.3)

Figure S29. Get High-res Image Gene #42: 'del_14q24.3' versus Clinical Feature #1: 'Time to Death'

'del_19q13.42' versus 'HISTOLOGICAL.TYPE'

P value = 3.05e-17 (Fisher's exact test), Q value = 8.7e-15

Table S30. Gene #44: 'del_19q13.42' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	123	99	137
DEL PEAK 25(19Q13.42) MUTATED	35	46	110
DEL PEAK 25(19Q13.42) WILD-TYPE	88	53	27

Figure S30. Get High-res Image Gene #44: 'del_19q13.42' 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 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)

[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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