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

Kidney Renal Clear Cell Carcinoma (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/C14M92Z9

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 31 focal events and 9 clinical features across 494 patients, 23 significant findings detected with Q value < 0.25.

amp_3q26.32 cnv correlated to 'NEOPLASM.DISEASESTAGE', 'PATHOLOGY.T.STAGE', and 'PATHOLOGY.M.STAGE'.
del_3q11.2 cnv correlated to 'GENDER'.
del_3p11.1 cnv correlated to 'GENDER'.
del_4q34.3 cnv correlated to 'Time to Death', 'NEOPLASM.DISEASESTAGE', and 'PATHOLOGY.T.STAGE'.
del_9p23 cnv correlated to 'Time to Death', 'NEOPLASM.DISEASESTAGE', and 'PATHOLOGY.T.STAGE'.
del_9p21.3 cnv correlated to 'Time to Death', 'NEOPLASM.DISEASESTAGE', 'PATHOLOGY.T.STAGE', 'PATHOLOGY.M.STAGE', and 'GENDER'.
del_10q23.31 cnv correlated to 'PATHOLOGY.T.STAGE'.
del_13q13.3 cnv correlated to 'Time to Death', 'NEOPLASM.DISEASESTAGE', and 'PATHOLOGY.T.STAGE'.
del_14q31.1 cnv correlated to 'NEOPLASM.DISEASESTAGE', 'PATHOLOGY.T.STAGE', and 'PATHOLOGY.N.STAGE'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 31 focal events and 9 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 23 significant findings detected.


		Clinical Features	Time to Death	AGE	NEOPLASM DISEASESTAGE	PATHOLOGY T STAGE	PATHOLOGY N STAGE	PATHOLOGY M STAGE	GENDER	KARNOFSKY PERFORMANCE SCORE	NUMBERPACKYEARSSMOKED
	nCNV (%)	nWild-Type	logrank test	t-test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	t-test	t-test
del 9p21 3	153 (31%)	341	3.4e-07 (8.28e-05)	0.043 (1.00)	2.26e-08 (5.59e-06)	1.26e-07 (3.09e-05)	0.029 (1.00)	0.000257 (0.0589)	0.000497 (0.112)	0.576 (1.00)
amp 3q26 32	84 (17%)	410	0.233 (1.00)	0.86 (1.00)	0.000116 (0.0269)	0.000268 (0.0611)	0.0593 (1.00)	0.000232 (0.0535)	0.454 (1.00)	0.152 (1.00)
del 4q34 3	78 (16%)	416	0.000278 (0.0632)	0.684 (1.00)	7.25e-06 (0.00175)	8.51e-07 (0.000207)	0.727 (1.00)	0.0264 (1.00)	0.517 (1.00)	0.193 (1.00)
del 9p23	145 (29%)	349	3.51e-05 (0.00827)	0.0238 (1.00)	2.81e-06 (0.00068)	1.6e-05 (0.00385)	0.0977 (1.00)	0.00265 (0.576)	0.00178 (0.397)	0.576 (1.00)
del 13q13 3	79 (16%)	415	0.000115 (0.0268)	0.594 (1.00)	0.000223 (0.0516)	2.23e-05 (0.0053)	0.204 (1.00)	0.0628 (1.00)	0.898 (1.00)	0.669 (1.00)
del 14q31 1	217 (44%)	277	0.00305 (0.659)	0.0547 (1.00)	2.63e-05 (0.00624)	0.000192 (0.0445)	0.000113 (0.0265)	0.00113 (0.254)	0.342 (1.00)	0.0872 (1.00)
del 3q11 2	150 (30%)	344	0.594 (1.00)	0.0947 (1.00)	0.746 (1.00)	0.103 (1.00)	0.601 (1.00)	1 (1.00)	6.44e-08 (1.58e-05)	0.703 (1.00)
del 3p11 1	222 (45%)	272	0.278 (1.00)	0.0328 (1.00)	0.557 (1.00)	0.697 (1.00)	1 (1.00)	0.386 (1.00)	1.74e-05 (0.00416)	0.727 (1.00)
del 10q23 31	93 (19%)	401	0.151 (1.00)	0.411 (1.00)	0.0122 (1.00)	0.000368 (0.0831)	1 (1.00)	0.43 (1.00)	0.053 (1.00)	0.775 (1.00)
amp 1q24 1	60 (12%)	434	0.0807 (1.00)	0.164 (1.00)	0.36 (1.00)	0.167 (1.00)	0.0751 (1.00)	0.342 (1.00)	0.666 (1.00)	0.499 (1.00)
amp 1q32 1	60 (12%)	434	0.174 (1.00)	0.0509 (1.00)	0.229 (1.00)	0.145 (1.00)	0.482 (1.00)	0.568 (1.00)	0.666 (1.00)	0.499 (1.00)
amp 4q32 1	16 (3%)	478	0.188 (1.00)	0.306 (1.00)	0.666 (1.00)	0.386 (1.00)	0.574 (1.00)	0.725 (1.00)	0.434 (1.00)	0.411 (1.00)
amp 5q35 1	314 (64%)	180	0.0171 (1.00)	0.0785 (1.00)	0.701 (1.00)	0.409 (1.00)	0.31 (1.00)	0.367 (1.00)	0.141 (1.00)	0.944 (1.00)
amp 7q36 3	168 (34%)	326	0.763 (1.00)	0.752 (1.00)	0.0163 (1.00)	0.0619 (1.00)	0.447 (1.00)	0.00256 (0.558)	0.0282 (1.00)	0.57 (1.00)
amp 8q24 22	76 (15%)	418	0.0772 (1.00)	0.00556 (1.00)	0.00248 (0.544)	0.00209 (0.463)	0.74 (1.00)	0.0398 (1.00)	0.19 (1.00)	0.297 (1.00)
amp 10p14	20 (4%)	474	0.81 (1.00)	0.0443 (1.00)	0.399 (1.00)	0.0321 (1.00)	0.216 (1.00)	0.533 (1.00)	0.812 (1.00)	0.887 (1.00)
amp 17q24 3	40 (8%)	454	0.185 (1.00)	0.0274 (1.00)	0.706 (1.00)	0.559 (1.00)	0.359 (1.00)	0.175 (1.00)	0.863 (1.00)	0.471 (1.00)
amp xp22 2	30 (6%)	464	0.624 (1.00)	0.865 (1.00)	0.0595 (1.00)	0.112 (1.00)	1 (1.00)	0.114 (1.00)	0.844 (1.00)	0.328 (1.00)
amp xp11 4	31 (6%)	463	0.942 (1.00)	0.819 (1.00)	0.0289 (1.00)	0.0927 (1.00)	1 (1.00)	0.0416 (1.00)	1 (1.00)	0.328 (1.00)
amp xq11 2	27 (5%)	467	0.575 (1.00)	0.347 (1.00)	0.345 (1.00)	0.35 (1.00)	1 (1.00)	0.409 (1.00)	0.836 (1.00)	0.328 (1.00)
amp xq28	33 (7%)	461	0.578 (1.00)	0.452 (1.00)	0.507 (1.00)	0.704 (1.00)	1 (1.00)	0.209 (1.00)	0.573 (1.00)	0.328 (1.00)
del 1p36 23	100 (20%)	394	0.017 (1.00)	0.158 (1.00)	0.351 (1.00)	0.0981 (1.00)	1 (1.00)	0.216 (1.00)	0.127 (1.00)	0.513 (1.00)
del 1p31 1	75 (15%)	419	0.14 (1.00)	0.137 (1.00)	0.673 (1.00)	0.0396 (1.00)	0.494 (1.00)	0.608 (1.00)	0.0359 (1.00)	0.513 (1.00)
del 1q43	40 (8%)	454	0.768 (1.00)	0.677 (1.00)	1 (1.00)	0.168 (1.00)	1 (1.00)	0.82 (1.00)	1 (1.00)	0.484 (1.00)
del 2q37 3	48 (10%)	446	0.814 (1.00)	0.912 (1.00)	0.443 (1.00)	0.628 (1.00)	1 (1.00)	0.403 (1.00)	0.154 (1.00)
del 3p25 3	435 (88%)	59	0.71 (1.00)	0.506 (1.00)	0.0619 (1.00)	0.00197 (0.437)	1 (1.00)	0.848 (1.00)	0.56 (1.00)	0.0535 (1.00)
del 3p24 3	436 (88%)	58	0.525 (1.00)	0.532 (1.00)	0.0728 (1.00)	0.00234 (0.515)	1 (1.00)	0.848 (1.00)	0.463 (1.00)	0.0535 (1.00)
del 3p12 3	313 (63%)	181	0.885 (1.00)	0.935 (1.00)	0.396 (1.00)	0.0591 (1.00)	0.616 (1.00)	0.7 (1.00)	0.0032 (0.688)	0.963 (1.00)
del 6q26	145 (29%)	349	0.806 (1.00)	0.328 (1.00)	0.308 (1.00)	0.588 (1.00)	0.00896 (1.00)	0.5 (1.00)	0.0223 (1.00)	0.197 (1.00)
del 6q26	145 (29%)	349	0.831 (1.00)	0.26 (1.00)	0.308 (1.00)	0.588 (1.00)	0.00896 (1.00)	0.5 (1.00)	0.0126 (1.00)	0.197 (1.00)
del 8p23 2	149 (30%)	345	0.0494 (1.00)	0.143 (1.00)	0.137 (1.00)	0.167 (1.00)	1 (1.00)	0.137 (1.00)	0.356 (1.00)	0.802 (1.00)

'amp_3q26.32' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.000116 (Fisher's exact test), Q value = 0.027

Table S1. Gene #3: 'amp_3q26.32' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	237	54	125	78
AMP PEAK 3(3Q26.32) MUTATED	26	6	27	25
AMP PEAK 3(3Q26.32) WILD-TYPE	211	48	98	53

Figure S1. Get High-res Image Gene #3: 'amp_3q26.32' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'amp_3q26.32' versus 'PATHOLOGY.T.STAGE'

P value = 0.000268 (Fisher's exact test), Q value = 0.061

Table S2. Gene #3: 'amp_3q26.32' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3	T4
ALL	242	65	176	11
AMP PEAK 3(3Q26.32) MUTATED	27	8	45	4
AMP PEAK 3(3Q26.32) WILD-TYPE	215	57	131	7

Figure S2. Get High-res Image Gene #3: 'amp_3q26.32' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'amp_3q26.32' versus 'PATHOLOGY.M.STAGE'

P value = 0.000232 (Fisher's exact test), Q value = 0.053

Table S3. Gene #3: 'amp_3q26.32' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

nPatients	M0	M1
ALL	417	77
AMP PEAK 3(3Q26.32) MUTATED	59	25
AMP PEAK 3(3Q26.32) WILD-TYPE	358	52

Figure S3. Get High-res Image Gene #3: 'amp_3q26.32' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

'del_3q11.2' versus 'GENDER'

P value = 6.44e-08 (Fisher's exact test), Q value = 1.6e-05

Table S4. Gene #21: 'del_3q11.2' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	171	323
DEL PEAK 8(3Q11.2) MUTATED	26	124
DEL PEAK 8(3Q11.2) WILD-TYPE	145	199

Figure S4. Get High-res Image Gene #21: 'del_3q11.2' versus Clinical Feature #7: 'GENDER'

'del_3p11.1' versus 'GENDER'

P value = 1.74e-05 (Fisher's exact test), Q value = 0.0042

Table S5. Gene #22: 'del_3p11.1' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	171	323
DEL PEAK 9(3P11.1) MUTATED	54	168
DEL PEAK 9(3P11.1) WILD-TYPE	117	155

Figure S5. Get High-res Image Gene #22: 'del_3p11.1' versus Clinical Feature #7: 'GENDER'

'del_4q34.3' versus 'Time to Death'

P value = 0.000278 (logrank test), Q value = 0.063

Table S6. Gene #23: 'del_4q34.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	493	163	0.1 - 120.6 (36.8)
DEL PEAK 10(4Q34.3) MUTATED	78	40	0.6 - 112.8 (33.0)
DEL PEAK 10(4Q34.3) WILD-TYPE	415	123	0.1 - 120.6 (37.0)

Figure S6. Get High-res Image Gene #23: 'del_4q34.3' versus Clinical Feature #1: 'Time to Death'

'del_4q34.3' versus 'NEOPLASM.DISEASESTAGE'

P value = 7.25e-06 (Fisher's exact test), Q value = 0.0017

Table S7. Gene #23: 'del_4q34.3' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	237	54	125	78
DEL PEAK 10(4Q34.3) MUTATED	19	7	31	21
DEL PEAK 10(4Q34.3) WILD-TYPE	218	47	94	57

Figure S7. Get High-res Image Gene #23: 'del_4q34.3' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'del_4q34.3' versus 'PATHOLOGY.T.STAGE'

P value = 8.51e-07 (Fisher's exact test), Q value = 0.00021

Table S8. Gene #23: 'del_4q34.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3	T4
ALL	242	65	176	11
DEL PEAK 10(4Q34.3) MUTATED	20	9	43	6
DEL PEAK 10(4Q34.3) WILD-TYPE	222	56	133	5

Figure S8. Get High-res Image Gene #23: 'del_4q34.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_9p23' versus 'Time to Death'

P value = 3.51e-05 (logrank test), Q value = 0.0083

Table S9. Gene #27: 'del_9p23' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	493	163	0.1 - 120.6 (36.8)
DEL PEAK 14(9P23) MUTATED	145	68	0.2 - 109.9 (36.2)
DEL PEAK 14(9P23) WILD-TYPE	348	95	0.1 - 120.6 (37.0)

Figure S9. Get High-res Image Gene #27: 'del_9p23' versus Clinical Feature #1: 'Time to Death'

'del_9p23' versus 'NEOPLASM.DISEASESTAGE'

P value = 2.81e-06 (Fisher's exact test), Q value = 0.00068

Table S10. Gene #27: 'del_9p23' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	237	54	125	78
DEL PEAK 14(9P23) MUTATED	47	12	51	35
DEL PEAK 14(9P23) WILD-TYPE	190	42	74	43

Figure S10. Get High-res Image Gene #27: 'del_9p23' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'del_9p23' versus 'PATHOLOGY.T.STAGE'

P value = 1.6e-05 (Fisher's exact test), Q value = 0.0039

Table S11. Gene #27: 'del_9p23' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3	T4
ALL	242	65	176	11
DEL PEAK 14(9P23) MUTATED	50	16	74	5
DEL PEAK 14(9P23) WILD-TYPE	192	49	102	6

Figure S11. Get High-res Image Gene #27: 'del_9p23' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_9p21.3' versus 'Time to Death'

P value = 3.4e-07 (logrank test), Q value = 8.3e-05

Table S12. Gene #28: 'del_9p21.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	493	163	0.1 - 120.6 (36.8)
DEL PEAK 15(9P21.3) MUTATED	153	75	0.2 - 109.9 (31.8)
DEL PEAK 15(9P21.3) WILD-TYPE	340	88	0.1 - 120.6 (37.2)

Figure S12. Get High-res Image Gene #28: 'del_9p21.3' versus Clinical Feature #1: 'Time to Death'

'del_9p21.3' versus 'NEOPLASM.DISEASESTAGE'

P value = 2.26e-08 (Fisher's exact test), Q value = 5.6e-06

Table S13. Gene #28: 'del_9p21.3' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	237	54	125	78
DEL PEAK 15(9P21.3) MUTATED	48	11	55	39
DEL PEAK 15(9P21.3) WILD-TYPE	189	43	70	39

Figure S13. Get High-res Image Gene #28: 'del_9p21.3' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'del_9p21.3' versus 'PATHOLOGY.T.STAGE'

P value = 1.26e-07 (Fisher's exact test), Q value = 3.1e-05

Table S14. Gene #28: 'del_9p21.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3	T4
ALL	242	65	176	11
DEL PEAK 15(9P21.3) MUTATED	51	15	81	6
DEL PEAK 15(9P21.3) WILD-TYPE	191	50	95	5

Figure S14. Get High-res Image Gene #28: 'del_9p21.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_9p21.3' versus 'PATHOLOGY.M.STAGE'

P value = 0.000257 (Fisher's exact test), Q value = 0.059

Table S15. Gene #28: 'del_9p21.3' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

nPatients	M0	M1
ALL	417	77
DEL PEAK 15(9P21.3) MUTATED	115	38
DEL PEAK 15(9P21.3) WILD-TYPE	302	39

Figure S15. Get High-res Image Gene #28: 'del_9p21.3' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

'del_9p21.3' versus 'GENDER'

P value = 0.000497 (Fisher's exact test), Q value = 0.11

Table S16. Gene #28: 'del_9p21.3' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	171	323
DEL PEAK 15(9P21.3) MUTATED	36	117
DEL PEAK 15(9P21.3) WILD-TYPE	135	206

Figure S16. Get High-res Image Gene #28: 'del_9p21.3' versus Clinical Feature #7: 'GENDER'

'del_10q23.31' versus 'PATHOLOGY.T.STAGE'

P value = 0.000368 (Fisher's exact test), Q value = 0.083

Table S17. Gene #29: 'del_10q23.31' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3	T4
ALL	242	65	176	11
DEL PEAK 16(10Q23.31) MUTATED	31	12	44	6
DEL PEAK 16(10Q23.31) WILD-TYPE	211	53	132	5

Figure S17. Get High-res Image Gene #29: 'del_10q23.31' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_13q13.3' versus 'Time to Death'

P value = 0.000115 (logrank test), Q value = 0.027

Table S18. Gene #30: 'del_13q13.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	493	163	0.1 - 120.6 (36.8)
DEL PEAK 17(13Q13.3) MUTATED	79	37	0.2 - 89.4 (27.0)
DEL PEAK 17(13Q13.3) WILD-TYPE	414	126	0.1 - 120.6 (37.4)

Figure S18. Get High-res Image Gene #30: 'del_13q13.3' versus Clinical Feature #1: 'Time to Death'

'del_13q13.3' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.000223 (Fisher's exact test), Q value = 0.052

Table S19. Gene #30: 'del_13q13.3' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	237	54	125	78
DEL PEAK 17(13Q13.3) MUTATED	25	4	30	20
DEL PEAK 17(13Q13.3) WILD-TYPE	212	50	95	58

Figure S19. Get High-res Image Gene #30: 'del_13q13.3' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'del_13q13.3' versus 'PATHOLOGY.T.STAGE'

P value = 2.23e-05 (Fisher's exact test), Q value = 0.0053

Table S20. Gene #30: 'del_13q13.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3	T4
ALL	242	65	176	11
DEL PEAK 17(13Q13.3) MUTATED	27	5	41	6
DEL PEAK 17(13Q13.3) WILD-TYPE	215	60	135	5

Figure S20. Get High-res Image Gene #30: 'del_13q13.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_14q31.1' versus 'NEOPLASM.DISEASESTAGE'

P value = 2.63e-05 (Fisher's exact test), Q value = 0.0062

Table S21. Gene #31: 'del_14q31.1' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	237	54	125	78
DEL PEAK 18(14Q31.1) MUTATED	78	27	66	46
DEL PEAK 18(14Q31.1) WILD-TYPE	159	27	59	32

Figure S21. Get High-res Image Gene #31: 'del_14q31.1' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'del_14q31.1' versus 'PATHOLOGY.T.STAGE'

P value = 0.000192 (Fisher's exact test), Q value = 0.045

Table S22. Gene #31: 'del_14q31.1' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients	T1	T2	T3	T4
ALL	242	65	176	11
DEL PEAK 18(14Q31.1) MUTATED	83	35	95	4
DEL PEAK 18(14Q31.1) WILD-TYPE	159	30	81	7

Figure S22. Get High-res Image Gene #31: 'del_14q31.1' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_14q31.1' versus 'PATHOLOGY.N.STAGE'

P value = 0.000113 (Fisher's exact test), Q value = 0.027

Table S23. Gene #31: 'del_14q31.1' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

nPatients	0	1
ALL	228	18
DEL PEAK 18(14Q31.1) MUTATED	96	16
DEL PEAK 18(14Q31.1) WILD-TYPE	132	2

Figure S23. Get High-res Image Gene #31: 'del_14q31.1' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Clinical data file = KIRC-TP.merged_data.txt
Number of patients = 494
Number of significantly focal cnvs = 31
Number of selected clinical features = 9
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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