Correlation between copy number variation genes (focal events) and selected clinical features

Brain Lower Grade Glioma (Primary solid tumor)

15 January 2014 | analyses__2014_01_15

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/C1N58JT3

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 45 focal events and 6 clinical features across 276 patients, 22 significant findings detected with Q value < 0.25.

amp_1q22 cnv correlated to 'AGE'.
amp_1q32.1 cnv correlated to 'AGE'.
amp_3q26.32 cnv correlated to 'Time to Death'.
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_12q14.1 cnv correlated to 'Time to Death'.
amp_17q24.3 cnv correlated to 'Time to Death'.
amp_19q13.2 cnv correlated to 'Time to Death' and 'AGE'.
del_1p36.31 cnv correlated to 'AGE' and 'HISTOLOGICAL.TYPE'.
del_1p32.3 cnv correlated to 'AGE' and 'HISTOLOGICAL.TYPE'.
del_6p25.3 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' and 'AGE'.
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 45 focal events and 6 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 22 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 7p11 2	72 (26%)	204	0.000232 (0.0593)	1.11e-05 (0.00287)	0.13 (1.00)	0.147 (1.00)	0.0719 (1.00)	0.66 (1.00)
amp 19q13 2	18 (7%)	258	8.98e-06 (0.00235)	4.18e-06 (0.0011)	1 (1.00)	0.223 (1.00)	0.414 (1.00)	0.298 (1.00)
del 1p36 31	107 (39%)	169	0.74 (1.00)	4.97e-05 (0.0128)	0.265 (1.00)	0.379 (1.00)	7.74e-18 (2.08e-15)	0.0882 (1.00)
del 1p32 3	100 (36%)	176	0.108 (1.00)	0.000458 (0.116)	0.379 (1.00)	0.61 (1.00)	5.21e-19 (1.41e-16)	0.0158 (1.00)
del 9p21 3	92 (33%)	184	8.29e-08 (2.21e-05)	7.44e-05 (0.0191)	0.798 (1.00)	0.176 (1.00)	0.0268 (1.00)	0.0062 (1.00)
del 10q26 3	79 (29%)	197	3.21e-06 (0.000848)	0.000853 (0.213)	0.0834 (1.00)	0.572 (1.00)	0.00659 (1.00)	0.888 (1.00)
amp 1q22	26 (9%)	250	0.0236 (1.00)	0.000875 (0.218)	0.416 (1.00)	0.92 (1.00)	0.634 (1.00)	0.511 (1.00)
amp 1q32 1	28 (10%)	248	0.00176 (0.432)	1.23e-06 (0.000328)	0.693 (1.00)	0.0375 (1.00)	0.324 (1.00)	0.208 (1.00)
amp 3q26 32	14 (5%)	262	0.000724 (0.183)	0.206 (1.00)	0.789 (1.00)	0.708 (1.00)	0.0326 (1.00)	0.39 (1.00)
amp 7q31 2	97 (35%)	179	0.0267 (1.00)	1.06e-05 (0.00276)	0.0227 (1.00)	0.493 (1.00)	0.0697 (1.00)	0.686 (1.00)
amp 7q32 3	102 (37%)	174	0.0408 (1.00)	2.79e-06 (0.000741)	0.0127 (1.00)	0.589 (1.00)	0.12 (1.00)	0.595 (1.00)
amp 12q14 1	19 (7%)	257	1.44e-05 (0.00374)	0.0131 (1.00)	0.636 (1.00)	0.274 (1.00)	0.0843 (1.00)	0.322 (1.00)
amp 17q24 3	18 (7%)	258	0.000759 (0.19)	0.246 (1.00)	0.628 (1.00)	0.524 (1.00)	0.908 (1.00)	1 (1.00)
del 6p25 3	28 (10%)	248	9.25e-05 (0.0237)	0.278 (1.00)	1 (1.00)	0.3 (1.00)	0.092 (1.00)	1 (1.00)
del 14q24 3	59 (21%)	217	0.000339 (0.0862)	0.112 (1.00)	0.0268 (1.00)	0.825 (1.00)	0.0964 (1.00)	0.351 (1.00)
del 19q13 42	146 (53%)	130	0.0512 (1.00)	0.529 (1.00)	1 (1.00)	0.844 (1.00)	1.24e-10 (3.31e-08)	0.897 (1.00)
amp 2p24 3	8 (3%)	268	0.59 (1.00)	0.384 (1.00)	0.477 (1.00)	0.516 (1.00)	0.734 (1.00)	1 (1.00)
amp 4q12	14 (5%)	262	0.067 (1.00)	0.273 (1.00)	1 (1.00)	0.637 (1.00)	0.0195 (1.00)	1 (1.00)
amp 6q21	6 (2%)	270	0.0249 (1.00)	0.546 (1.00)	1 (1.00)	0.0178 (1.00)	0.156 (1.00)	0.0874 (1.00)
amp 8q24 13	58 (21%)	218	0.869 (1.00)	0.511 (1.00)	0.104 (1.00)	0.841 (1.00)	0.00385 (0.932)	0.875 (1.00)
amp 9q34 3	28 (10%)	248	0.225 (1.00)	0.729 (1.00)	0.112 (1.00)	0.334 (1.00)	0.0414 (1.00)	0.674 (1.00)
amp 10p15 2	41 (15%)	235	0.538 (1.00)	0.0021 (0.515)	0.0611 (1.00)	0.18 (1.00)	0.00271 (0.661)	0.205 (1.00)
amp 11q23 3	47 (17%)	229	0.846 (1.00)	0.264 (1.00)	0.748 (1.00)	0.438 (1.00)	0.759 (1.00)	1 (1.00)
amp 12p13 32	46 (17%)	230	0.419 (1.00)	0.25 (1.00)	0.0523 (1.00)	0.226 (1.00)	0.41 (1.00)	0.301 (1.00)
amp 13q34	13 (5%)	263	0.402 (1.00)	0.929 (1.00)	0.394 (1.00)	0.854 (1.00)	0.517 (1.00)	1 (1.00)
amp 19p13 3	66 (24%)	210	0.786 (1.00)	0.0409 (1.00)	1 (1.00)	0.671 (1.00)	0.00116 (0.287)	1 (1.00)
amp xp11 22	37 (13%)	239	0.625 (1.00)	0.796 (1.00)	0.376 (1.00)	0.963 (1.00)	0.00602 (1.00)	0.708 (1.00)
del 1q44	16 (6%)	260	0.7 (1.00)	0.545 (1.00)	0.446 (1.00)	0.985 (1.00)	0.134 (1.00)	1 (1.00)
del 2q37 3	41 (15%)	235	0.923 (1.00)	0.0901 (1.00)	0.397 (1.00)	0.395 (1.00)	0.273 (1.00)	0.588 (1.00)
del 3p21 1	25 (9%)	251	0.0506 (1.00)	0.29 (1.00)	0.675 (1.00)	0.0442 (1.00)	0.297 (1.00)	0.114 (1.00)
del 3q29	24 (9%)	252	0.126 (1.00)	0.849 (1.00)	0.0908 (1.00)	0.895 (1.00)	0.0634 (1.00)	0.648 (1.00)
del 4q34 3	80 (29%)	196	0.783 (1.00)	0.209 (1.00)	0.69 (1.00)	0.613 (1.00)	0.303 (1.00)	0.396 (1.00)
del 5p15 33	32 (12%)	244	0.975 (1.00)	0.143 (1.00)	0.349 (1.00)	0.0846 (1.00)	0.00493 (1.00)	0.0709 (1.00)
del 5q33 3	37 (13%)	239	0.0387 (1.00)	0.828 (1.00)	1 (1.00)	0.726 (1.00)	0.0587 (1.00)	0.453 (1.00)
del 6q24 3	46 (17%)	230	0.0044 (1.00)	0.325 (1.00)	0.419 (1.00)	0.5 (1.00)	0.00126 (0.311)	0.491 (1.00)
del 11p15 5	61 (22%)	215	0.217 (1.00)	0.0641 (1.00)	0.19 (1.00)	0.322 (1.00)	0.00406 (0.978)	1 (1.00)
del 11q25	22 (8%)	254	0.0804 (1.00)	0.858 (1.00)	1 (1.00)	0.215 (1.00)	0.168 (1.00)	0.812 (1.00)
del 12q12	37 (13%)	239	0.957 (1.00)	0.958 (1.00)	0.595 (1.00)	0.895 (1.00)	0.00325 (0.789)	1 (1.00)
del 13q21 2	83 (30%)	193	0.161 (1.00)	0.712 (1.00)	0.431 (1.00)	0.0886 (1.00)	0.102 (1.00)	0.4 (1.00)
del 13q34	61 (22%)	215	0.0901 (1.00)	0.813 (1.00)	1 (1.00)	0.936 (1.00)	0.668 (1.00)	0.352 (1.00)
del 17q25 3	15 (5%)	261	0.896 (1.00)	0.423 (1.00)	0.791 (1.00)	0.196 (1.00)	0.893 (1.00)	0.573 (1.00)
del 18q23	43 (16%)	233	0.588 (1.00)	0.166 (1.00)	0.407 (1.00)	0.882 (1.00)	0.777 (1.00)	0.724 (1.00)
del 22q13 31	42 (15%)	234	0.0951 (1.00)	0.0754 (1.00)	0.867 (1.00)	0.117 (1.00)	0.0127 (1.00)	0.859 (1.00)
del xp21 1	53 (19%)	223	0.522 (1.00)	0.627 (1.00)	0.17 (1.00)	0.219 (1.00)	0.925 (1.00)	0.87 (1.00)
del xq21 1	36 (13%)	240	0.459 (1.00)	0.0933 (1.00)	0.72 (1.00)	0.843 (1.00)	0.184 (1.00)	0.851 (1.00)

'amp_1q22' versus 'AGE'

P value = 0.000875 (t-test), Q value = 0.22

Table S1. Gene #1: 'amp_1q22' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	276	43.1 (13.3)
AMP PEAK 1(1Q22) MUTATED	26	51.9 (12.7)
AMP PEAK 1(1Q22) WILD-TYPE	250	42.2 (13.1)

Figure S1. Get High-res Image Gene #1: 'amp_1q22' versus Clinical Feature #2: 'AGE'

'amp_1q32.1' versus 'AGE'

P value = 1.23e-06 (t-test), Q value = 0.00033

Table S2. Gene #2: 'amp_1q32.1' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	276	43.1 (13.3)
AMP PEAK 2(1Q32.1) MUTATED	28	55.3 (11.5)
AMP PEAK 2(1Q32.1) WILD-TYPE	248	41.7 (12.8)

Figure S2. Get High-res Image Gene #2: 'amp_1q32.1' versus Clinical Feature #2: 'AGE'

'amp_3q26.32' versus 'Time to Death'

P value = 0.000724 (logrank test), Q value = 0.18

Table S3. Gene #4: 'amp_3q26.32' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	275	59	0.0 - 211.2 (15.4)
AMP PEAK 4(3Q26.32) MUTATED	14	5	0.2 - 41.1 (9.7)
AMP PEAK 4(3Q26.32) WILD-TYPE	261	54	0.0 - 211.2 (15.5)

Figure S3. Get High-res Image Gene #4: 'amp_3q26.32' versus Clinical Feature #1: 'Time to Death'

'amp_7p11.2' versus 'Time to Death'

P value = 0.000232 (logrank test), Q value = 0.059

Table S4. Gene #7: 'amp_7p11.2' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	275	59	0.0 - 211.2 (15.4)
AMP PEAK 7(7P11.2) MUTATED	72	29	0.1 - 211.2 (15.5)
AMP PEAK 7(7P11.2) WILD-TYPE	203	30	0.0 - 182.3 (15.4)

Figure S4. Get High-res Image Gene #7: 'amp_7p11.2' versus Clinical Feature #1: 'Time to Death'

'amp_7p11.2' versus 'AGE'

P value = 1.11e-05 (t-test), Q value = 0.0029

Table S5. Gene #7: 'amp_7p11.2' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	276	43.1 (13.3)
AMP PEAK 7(7P11.2) MUTATED	72	49.3 (13.4)
AMP PEAK 7(7P11.2) WILD-TYPE	204	40.9 (12.6)

Figure S5. Get High-res Image Gene #7: 'amp_7p11.2' versus Clinical Feature #2: 'AGE'

'amp_7q31.2' versus 'AGE'

P value = 1.06e-05 (t-test), Q value = 0.0028

Table S6. Gene #8: 'amp_7q31.2' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	276	43.1 (13.3)
AMP PEAK 8(7Q31.2) MUTATED	97	47.9 (13.1)
AMP PEAK 8(7Q31.2) WILD-TYPE	179	40.5 (12.7)

Figure S6. Get High-res Image Gene #8: 'amp_7q31.2' versus Clinical Feature #2: 'AGE'

'amp_7q32.3' versus 'AGE'

P value = 2.79e-06 (t-test), Q value = 0.00074

Table S7. Gene #9: 'amp_7q32.3' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	276	43.1 (13.3)
AMP PEAK 9(7Q32.3) MUTATED	102	48.0 (13.0)
AMP PEAK 9(7Q32.3) WILD-TYPE	174	40.2 (12.7)

Figure S7. Get High-res Image Gene #9: 'amp_7q32.3' versus Clinical Feature #2: 'AGE'

'amp_12q14.1' versus 'Time to Death'

P value = 1.44e-05 (logrank test), Q value = 0.0037

Table S8. Gene #15: 'amp_12q14.1' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	275	59	0.0 - 211.2 (15.4)
AMP PEAK 15(12Q14.1) MUTATED	19	10	1.2 - 80.0 (15.0)
AMP PEAK 15(12Q14.1) WILD-TYPE	256	49	0.0 - 211.2 (15.5)

Figure S8. Get High-res Image Gene #15: 'amp_12q14.1' versus Clinical Feature #1: 'Time to Death'

'amp_17q24.3' versus 'Time to Death'

P value = 0.000759 (logrank test), Q value = 0.19

Table S9. Gene #17: 'amp_17q24.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	275	59	0.0 - 211.2 (15.4)
AMP PEAK 17(17Q24.3) MUTATED	18	9	6.0 - 78.2 (17.6)
AMP PEAK 17(17Q24.3) WILD-TYPE	257	50	0.0 - 211.2 (15.1)

Figure S9. Get High-res Image Gene #17: 'amp_17q24.3' versus Clinical Feature #1: 'Time to Death'

'amp_19q13.2' versus 'Time to Death'

P value = 8.98e-06 (logrank test), Q value = 0.0024

Table S10. Gene #19: 'amp_19q13.2' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	275	59	0.0 - 211.2 (15.4)
AMP PEAK 19(19Q13.2) MUTATED	18	7	0.0 - 43.9 (14.1)
AMP PEAK 19(19Q13.2) WILD-TYPE	257	52	0.1 - 211.2 (15.7)

Figure S10. Get High-res Image Gene #19: 'amp_19q13.2' versus Clinical Feature #1: 'Time to Death'

'amp_19q13.2' versus 'AGE'

P value = 4.18e-06 (t-test), Q value = 0.0011

Table S11. Gene #19: 'amp_19q13.2' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	276	43.1 (13.3)
AMP PEAK 19(19Q13.2) MUTATED	18	54.6 (8.1)
AMP PEAK 19(19Q13.2) WILD-TYPE	258	42.3 (13.3)

Figure S11. Get High-res Image Gene #19: 'amp_19q13.2' versus Clinical Feature #2: 'AGE'

'del_1p36.31' versus 'AGE'

P value = 4.97e-05 (t-test), Q value = 0.013

Table S12. Gene #21: 'del_1p36.31' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	276	43.1 (13.3)
DEL PEAK 1(1P36.31) MUTATED	107	47.2 (13.1)
DEL PEAK 1(1P36.31) WILD-TYPE	169	40.5 (12.8)

Figure S12. Get High-res Image Gene #21: 'del_1p36.31' versus Clinical Feature #2: 'AGE'

'del_1p36.31' versus 'HISTOLOGICAL.TYPE'

P value = 7.74e-18 (Fisher's exact test), Q value = 2.1e-15

Table S13. Gene #21: 'del_1p36.31' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	88	76	112
DEL PEAK 1(1P36.31) MUTATED	10	20	77
DEL PEAK 1(1P36.31) WILD-TYPE	78	56	35

Figure S13. Get High-res Image Gene #21: 'del_1p36.31' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'del_1p32.3' versus 'AGE'

P value = 0.000458 (t-test), Q value = 0.12

Table S14. Gene #22: 'del_1p32.3' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	276	43.1 (13.3)
DEL PEAK 2(1P32.3) MUTATED	100	46.8 (13.0)
DEL PEAK 2(1P32.3) WILD-TYPE	176	41.0 (13.1)

Figure S14. Get High-res Image Gene #22: 'del_1p32.3' versus Clinical Feature #2: 'AGE'

'del_1p32.3' versus 'HISTOLOGICAL.TYPE'

P value = 5.21e-19 (Fisher's exact test), Q value = 1.4e-16

Table S15. Gene #22: 'del_1p32.3' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	88	76	112
DEL PEAK 2(1P32.3) MUTATED	8	17	75
DEL PEAK 2(1P32.3) WILD-TYPE	80	59	37

Figure S15. Get High-res Image Gene #22: 'del_1p32.3' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'del_6p25.3' versus 'Time to Death'

P value = 9.25e-05 (logrank test), Q value = 0.024

Table S16. Gene #30: 'del_6p25.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	275	59	0.0 - 211.2 (15.4)
DEL PEAK 10(6P25.3) MUTATED	28	11	0.2 - 94.5 (16.8)
DEL PEAK 10(6P25.3) WILD-TYPE	247	48	0.0 - 211.2 (15.3)

Figure S16. Get High-res Image Gene #30: 'del_6p25.3' versus Clinical Feature #1: 'Time to Death'

'del_9p21.3' versus 'Time to Death'

P value = 8.29e-08 (logrank test), Q value = 2.2e-05

Table S17. Gene #32: 'del_9p21.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	275	59	0.0 - 211.2 (15.4)
DEL PEAK 12(9P21.3) MUTATED	92	32	0.1 - 117.4 (14.8)
DEL PEAK 12(9P21.3) WILD-TYPE	183	27	0.0 - 211.2 (15.4)

Figure S17. Get High-res Image Gene #32: 'del_9p21.3' versus Clinical Feature #1: 'Time to Death'

'del_9p21.3' versus 'AGE'

P value = 7.44e-05 (t-test), Q value = 0.019

Table S18. Gene #32: 'del_9p21.3' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	276	43.1 (13.3)
DEL PEAK 12(9P21.3) MUTATED	92	47.6 (13.2)
DEL PEAK 12(9P21.3) WILD-TYPE	184	40.9 (12.9)

Figure S18. Get High-res Image Gene #32: 'del_9p21.3' versus Clinical Feature #2: 'AGE'

'del_10q26.3' versus 'Time to Death'

P value = 3.21e-06 (logrank test), Q value = 0.00085

Table S19. Gene #33: 'del_10q26.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	275	59	0.0 - 211.2 (15.4)
DEL PEAK 13(10Q26.3) MUTATED	79	34	0.1 - 156.2 (16.0)
DEL PEAK 13(10Q26.3) WILD-TYPE	196	25	0.0 - 211.2 (15.1)

Figure S19. Get High-res Image Gene #33: 'del_10q26.3' versus Clinical Feature #1: 'Time to Death'

'del_10q26.3' versus 'AGE'

P value = 0.000853 (t-test), Q value = 0.21

Table S20. Gene #33: 'del_10q26.3' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	276	43.1 (13.3)
DEL PEAK 13(10Q26.3) MUTATED	79	47.5 (13.8)
DEL PEAK 13(10Q26.3) WILD-TYPE	197	41.4 (12.8)

Figure S20. Get High-res Image Gene #33: 'del_10q26.3' versus Clinical Feature #2: 'AGE'

'del_14q24.3' versus 'Time to Death'

P value = 0.000339 (logrank test), Q value = 0.086

Table S21. Gene #39: 'del_14q24.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	275	59	0.0 - 211.2 (15.4)
DEL PEAK 19(14Q24.3) MUTATED	59	24	0.2 - 130.8 (17.5)
DEL PEAK 19(14Q24.3) WILD-TYPE	216	35	0.0 - 211.2 (14.9)

Figure S21. Get High-res Image Gene #39: 'del_14q24.3' versus Clinical Feature #1: 'Time to Death'

'del_19q13.42' versus 'HISTOLOGICAL.TYPE'

P value = 1.24e-10 (Fisher's exact test), Q value = 3.3e-08

Table S22. Gene #42: 'del_19q13.42' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	ASTROCYTOMA	OLIGOASTROCYTOMA	OLIGODENDROGLIOMA
ALL	88	76	112
DEL PEAK 22(19Q13.42) MUTATED	29	31	86
DEL PEAK 22(19Q13.42) WILD-TYPE	59	45	26

Figure S22. Get High-res Image Gene #42: '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 = 276
Number of significantly focal cnvs = 45
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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