Kidney Renal Clear Cell Carcinoma: Correlation between copy number variation genes and selected clinical features<BR>(primary solid tumor cohort)

Kidney Renal Clear Cell Carcinoma: Correlation between copy number variation genes and selected clinical features
(primary solid tumor cohort)

Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)

Overview

Introduction

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

Summary

Testing the association between copy number variation of 30 peak regions and 8 clinical features across 493 patients, 26 significant findings detected with Q value < 0.25.

Amp Peak 3(3q26.32) cnvs correlated to 'PATHOLOGY.T', 'PATHOLOGICSPREAD(M)', and 'TUMOR.STAGE'.
Amp Peak 7(8q24.22) cnvs correlated to 'PATHOLOGY.T'.
Del Peak 6(3p21.32) cnvs correlated to 'PATHOLOGY.T' and 'TUMOR.STAGE'.
Del Peak 8(3q11.2) cnvs correlated to 'GENDER'.
Del Peak 9(4q34.3) cnvs correlated to 'Time to Death', 'PATHOLOGY.T', and 'TUMOR.STAGE'.
Del Peak 13(9p23) cnvs correlated to 'Time to Death', 'PATHOLOGY.T', 'PATHOLOGICSPREAD(M)', and 'TUMOR.STAGE'.
Del Peak 14(9p21.3) cnvs correlated to 'Time to Death', 'PATHOLOGY.T', 'PATHOLOGICSPREAD(M)', and 'TUMOR.STAGE'.
Del Peak 15(10q23.31) cnvs correlated to 'PATHOLOGY.T'.
Del Peak 16(13q13.3) cnvs correlated to 'Time to Death', 'PATHOLOGY.T', and 'TUMOR.STAGE'.
Del Peak 17(14q31.1) cnvs correlated to 'PATHOLOGY.T', 'PATHOLOGY.N', 'PATHOLOGICSPREAD(M)', and 'TUMOR.STAGE'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 30 regions and 8 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 26 significant findings detected.


		Clinical Features	Time to Death	AGE	GENDER	KARNOFSKY PERFORMANCE SCORE	PATHOLOGY T	PATHOLOGY N	PATHOLOGICSPREAD(M)	TUMOR STAGE
	nCNV (%)	nWild-Type	logrank test	t-test	Fisher's exact test	t-test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
Del Peak 13(9p23)	144 (29%)	349	0.000138 (0.0304)	0.0136 (1.00)	0.00361 (0.744)	0.656 (1.00)	1.32e-05 (0.00302)	0.262 (1.00)	0.000876 (0.187)	5.35e-06 (0.00123)
Del Peak 14(9p21 3)	152 (31%)	341	2.03e-06 (0.000473)	0.0261 (1.00)	0.00144 (0.303)	0.656 (1.00)	9.4e-08 (2.22e-05)	0.0589 (1.00)	6.93e-05 (0.0156)	3.19e-08 (7.57e-06)
Del Peak 17(14q31 1)	218 (44%)	275	0.00179 (0.374)	0.055 (1.00)	0.393 (1.00)	0.0872 (1.00)	0.000106 (0.0236)	0.000113 (0.0249)	0.00101 (0.216)	2.36e-05 (0.00537)
Amp Peak 3(3q26 32)	80 (16%)	413	0.156 (1.00)	0.903 (1.00)	0.442 (1.00)	0.152 (1.00)	9.88e-05 (0.022)	0.0593 (1.00)	7.09e-05 (0.0159)	2.32e-05 (0.00529)
Del Peak 9(4q34 3)	76 (15%)	417	0.000557 (0.12)	0.568 (1.00)	0.433 (1.00)	0.0261 (1.00)	3.5e-07 (8.2e-05)	1 (1.00)	0.00862 (1.00)	2.36e-06 (0.000547)
Del Peak 16(13q13 3)	76 (15%)	417	0.000848 (0.182)	0.884 (1.00)	0.794 (1.00)	0.748 (1.00)	1.3e-05 (0.00299)	0.325 (1.00)	0.0377 (1.00)	0.000324 (0.0709)
Del Peak 6(3p21 32)	435 (88%)	58	0.498 (1.00)	0.704 (1.00)	0.772 (1.00)	0.0817 (1.00)	2.78e-05 (0.00629)	1 (1.00)	0.333 (1.00)	0.000492 (0.107)
Amp Peak 7(8q24 22)	73 (15%)	420	0.0527 (1.00)	0.0214 (1.00)	0.11 (1.00)	0.297 (1.00)	0.00108 (0.229)	0.74 (1.00)	0.053 (1.00)	0.00229 (0.473)
Del Peak 8(3q11 2)	150 (30%)	343	0.635 (1.00)	0.0111 (1.00)	1.32e-07 (3.1e-05)	0.749 (1.00)	0.132 (1.00)	0.787 (1.00)	0.591 (1.00)	0.45 (1.00)
Del Peak 15(10q23 31)	90 (18%)	403	0.217 (1.00)	0.209 (1.00)	0.0272 (1.00)	0.764 (1.00)	0.00045 (0.0982)	1 (1.00)	0.333 (1.00)	0.0174 (1.00)
Amp Peak 1(1q24 1)	60 (12%)	433	0.2 (1.00)	0.164 (1.00)	0.666 (1.00)	0.499 (1.00)	0.155 (1.00)	0.0751 (1.00)	0.339 (1.00)	0.298 (1.00)
Amp Peak 2(1q32 1)	59 (12%)	434	0.437 (1.00)	0.0725 (1.00)	0.771 (1.00)	0.499 (1.00)	0.162 (1.00)	0.482 (1.00)	0.703 (1.00)	0.239 (1.00)
Amp Peak 4(4q32 1)	14 (3%)	479	0.0584 (1.00)	0.416 (1.00)	0.258 (1.00)	0.411 (1.00)	0.231 (1.00)	0.574 (1.00)	0.462 (1.00)	0.415 (1.00)
Amp Peak 5(5q35 1)	311 (63%)	182	0.0454 (1.00)	0.0923 (1.00)	0.141 (1.00)	0.944 (1.00)	0.296 (1.00)	0.31 (1.00)	0.366 (1.00)	0.633 (1.00)
Amp Peak 6(7q36 3)	163 (33%)	330	0.724 (1.00)	0.806 (1.00)	0.0352 (1.00)	0.57 (1.00)	0.0564 (1.00)	0.443 (1.00)	0.00523 (1.00)	0.02 (1.00)
Amp Peak 8(10p14)	16 (3%)	477	0.234 (1.00)	0.423 (1.00)	0.594 (1.00)	0.887 (1.00)	0.0101 (1.00)	0.188 (1.00)	0.288 (1.00)	0.0495 (1.00)
Amp Peak 9(17q24 3)	37 (8%)	456	0.0512 (1.00)	0.0662 (1.00)	0.858 (1.00)	0.471 (1.00)	0.499 (1.00)	0.359 (1.00)	0.244 (1.00)	0.867 (1.00)
Amp Peak 10(Xp22 2)	35 (7%)	458	0.468 (1.00)	0.676 (1.00)	0.854 (1.00)	0.726 (1.00)	0.0803 (1.00)	0.668 (1.00)	0.0897 (1.00)	0.00984 (1.00)
Amp Peak 11(Xp11 4)	36 (7%)	457	0.759 (1.00)	0.712 (1.00)	0.857 (1.00)	0.726 (1.00)	0.0656 (1.00)	0.668 (1.00)	0.0509 (1.00)	0.00472 (0.968)
Amp Peak 12(Xq11 2)	32 (6%)	461	0.803 (1.00)	0.145 (1.00)	0.706 (1.00)	0.726 (1.00)	0.168 (1.00)	0.647 (1.00)	0.31 (1.00)	0.0563 (1.00)
Del Peak 1(1p36 23)	98 (20%)	395	0.0495 (1.00)	0.123 (1.00)	0.123 (1.00)	0.284 (1.00)	0.109 (1.00)	1 (1.00)	0.0844 (1.00)	0.168 (1.00)
Del Peak 2(1p31 1)	72 (15%)	421	0.219 (1.00)	0.0726 (1.00)	0.016 (1.00)	0.284 (1.00)	0.0532 (1.00)	0.722 (1.00)	0.294 (1.00)	0.179 (1.00)
Del Peak 3(1q43)	38 (8%)	455	0.704 (1.00)	0.335 (1.00)	1 (1.00)		0.0673 (1.00)	0.374 (1.00)	1 (1.00)	0.746 (1.00)
Del Peak 4(2q37 3)	48 (10%)	445	0.673 (1.00)	0.63 (1.00)	0.153 (1.00)		0.835 (1.00)	1 (1.00)	0.402 (1.00)	0.558 (1.00)
Del Peak 5(3p25 3)	432 (88%)	61	0.783 (1.00)	0.788 (1.00)	0.569 (1.00)	0.0817 (1.00)	0.00136 (0.287)	1 (1.00)	0.707 (1.00)	0.0125 (1.00)
Del Peak 7(3p12 2)	283 (57%)	210	0.614 (1.00)	0.761 (1.00)	0.00221 (0.461)	0.741 (1.00)	0.218 (1.00)	0.626 (1.00)	0.53 (1.00)	0.23 (1.00)
Del Peak 10(6q26)	142 (29%)	351	0.565 (1.00)	0.287 (1.00)	0.012 (1.00)	0.256 (1.00)	0.62 (1.00)	0.0195 (1.00)	0.41 (1.00)	0.319 (1.00)
Del Peak 11(6q26)	142 (29%)	351	0.589 (1.00)	0.226 (1.00)	0.00648 (1.00)	0.256 (1.00)	0.62 (1.00)	0.0195 (1.00)	0.41 (1.00)	0.319 (1.00)
Del Peak 12(8p23 2)	146 (30%)	347	0.0385 (1.00)	0.139 (1.00)	0.256 (1.00)	0.893 (1.00)	0.175 (1.00)	0.786 (1.00)	0.055 (1.00)	0.139 (1.00)
Del Peak 18(Xq23)	55 (11%)	438	0.287 (1.00)	0.669 (1.00)	0.234 (1.00)		0.295 (1.00)	0.657 (1.00)	0.168 (1.00)	0.139 (1.00)

'Amp Peak 3(3q26.32) mutation analysis' versus 'PATHOLOGY.T'

P value = 9.88e-05 (Fisher's exact test), Q value = 0.022

Table S1. Gene #3: 'Amp Peak 3(3q26.32) mutation analysis' versus Clinical Feature #5: 'PATHOLOGY.T'

nPatients	T1	T2	T3	T4
ALL	242	64	176	11
AMP PEAK 3(3Q26.32) MUTATED	24	8	44	4
AMP PEAK 3(3Q26.32) WILD-TYPE	218	56	132	7

Figure S1. Get High-res Image Gene #3: 'Amp Peak 3(3q26.32) mutation analysis' versus Clinical Feature #5: 'PATHOLOGY.T'

'Amp Peak 3(3q26.32) mutation analysis' versus 'PATHOLOGICSPREAD(M)'

P value = 7.09e-05 (Fisher's exact test), Q value = 0.016

Table S2. Gene #3: 'Amp Peak 3(3q26.32) mutation analysis' versus Clinical Feature #7: 'PATHOLOGICSPREAD(M)'

nPatients	M0	M1
ALL	417	76
AMP PEAK 3(3Q26.32) MUTATED	55	25
AMP PEAK 3(3Q26.32) WILD-TYPE	362	51

Figure S2. Get High-res Image Gene #3: 'Amp Peak 3(3q26.32) mutation analysis' versus Clinical Feature #7: 'PATHOLOGICSPREAD(M)'

'Amp Peak 3(3q26.32) mutation analysis' versus 'TUMOR.STAGE'

P value = 2.32e-05 (Fisher's exact test), Q value = 0.0053

Table S3. Gene #3: 'Amp Peak 3(3q26.32) mutation analysis' versus Clinical Feature #8: 'TUMOR.STAGE'

nPatients	I	II	III	IV
ALL	238	52	123	80
AMP PEAK 3(3Q26.32) MUTATED	23	6	25	26
AMP PEAK 3(3Q26.32) WILD-TYPE	215	46	98	54

Figure S3. Get High-res Image Gene #3: 'Amp Peak 3(3q26.32) mutation analysis' versus Clinical Feature #8: 'TUMOR.STAGE'

'Amp Peak 7(8q24.22) mutation analysis' versus 'PATHOLOGY.T'

P value = 0.00108 (Fisher's exact test), Q value = 0.23

Table S4. Gene #7: 'Amp Peak 7(8q24.22) mutation analysis' versus Clinical Feature #5: 'PATHOLOGY.T'

nPatients	T1	T2	T3	T4
ALL	242	64	176	11
AMP PEAK 7(8Q24.22) MUTATED	21	11	39	2
AMP PEAK 7(8Q24.22) WILD-TYPE	221	53	137	9

Figure S4. Get High-res Image Gene #7: 'Amp Peak 7(8q24.22) mutation analysis' versus Clinical Feature #5: 'PATHOLOGY.T'

'Del Peak 6(3p21.32) mutation analysis' versus 'PATHOLOGY.T'

P value = 2.78e-05 (Fisher's exact test), Q value = 0.0063

Table S5. Gene #18: 'Del Peak 6(3p21.32) mutation analysis' versus Clinical Feature #5: 'PATHOLOGY.T'

nPatients	T1	T2	T3	T4
ALL	242	64	176	11
DEL PEAK 6(3P21.32) MUTATED	209	52	168	6
DEL PEAK 6(3P21.32) WILD-TYPE	33	12	8	5

Figure S5. Get High-res Image Gene #18: 'Del Peak 6(3p21.32) mutation analysis' versus Clinical Feature #5: 'PATHOLOGY.T'

'Del Peak 6(3p21.32) mutation analysis' versus 'TUMOR.STAGE'

P value = 0.000492 (Fisher's exact test), Q value = 0.11

Table S6. Gene #18: 'Del Peak 6(3p21.32) mutation analysis' versus Clinical Feature #8: 'TUMOR.STAGE'

nPatients	I	II	III	IV
ALL	238	52	123	80
DEL PEAK 6(3P21.32) MUTATED	205	40	119	71
DEL PEAK 6(3P21.32) WILD-TYPE	33	12	4	9

Figure S6. Get High-res Image Gene #18: 'Del Peak 6(3p21.32) mutation analysis' versus Clinical Feature #8: 'TUMOR.STAGE'

'Del Peak 8(3q11.2) mutation analysis' versus 'GENDER'

P value = 1.32e-07 (Fisher's exact test), Q value = 3.1e-05

Table S7. Gene #20: 'Del Peak 8(3q11.2) mutation analysis' versus Clinical Feature #3: 'GENDER'

nPatients	FEMALE	MALE
ALL	322	171
DEL PEAK 8(3Q11.2) MUTATED	123	27
DEL PEAK 8(3Q11.2) WILD-TYPE	199	144

Figure S7. Get High-res Image Gene #20: 'Del Peak 8(3q11.2) mutation analysis' versus Clinical Feature #3: 'GENDER'

'Del Peak 9(4q34.3) mutation analysis' versus 'Time to Death'

P value = 0.000557 (logrank test), Q value = 0.12

Table S8. Gene #21: 'Del Peak 9(4q34.3) mutation analysis' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	490	158	0.1 - 111.0 (35.2)
DEL PEAK 9(4Q34.3) MUTATED	76	38	0.2 - 91.4 (35.1)
DEL PEAK 9(4Q34.3) WILD-TYPE	414	120	0.1 - 111.0 (35.2)

Figure S8. Get High-res Image Gene #21: 'Del Peak 9(4q34.3) mutation analysis' versus Clinical Feature #1: 'Time to Death'

'Del Peak 9(4q34.3) mutation analysis' versus 'PATHOLOGY.T'

P value = 3.5e-07 (Fisher's exact test), Q value = 8.2e-05

Table S9. Gene #21: 'Del Peak 9(4q34.3) mutation analysis' versus Clinical Feature #5: 'PATHOLOGY.T'

nPatients	T1	T2	T3	T4
ALL	242	64	176	11
DEL PEAK 9(4Q34.3) MUTATED	19	8	43	6
DEL PEAK 9(4Q34.3) WILD-TYPE	223	56	133	5

Figure S9. Get High-res Image Gene #21: 'Del Peak 9(4q34.3) mutation analysis' versus Clinical Feature #5: 'PATHOLOGY.T'

'Del Peak 9(4q34.3) mutation analysis' versus 'TUMOR.STAGE'

P value = 2.36e-06 (Fisher's exact test), Q value = 0.00055

Table S10. Gene #21: 'Del Peak 9(4q34.3) mutation analysis' versus Clinical Feature #8: 'TUMOR.STAGE'

nPatients	I	II	III	IV
ALL	238	52	123	80
DEL PEAK 9(4Q34.3) MUTATED	18	6	30	22
DEL PEAK 9(4Q34.3) WILD-TYPE	220	46	93	58

Figure S10. Get High-res Image Gene #21: 'Del Peak 9(4q34.3) mutation analysis' versus Clinical Feature #8: 'TUMOR.STAGE'

'Del Peak 13(9p23) mutation analysis' versus 'Time to Death'

P value = 0.000138 (logrank test), Q value = 0.03

Table S11. Gene #25: 'Del Peak 13(9p23) mutation analysis' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	490	158	0.1 - 111.0 (35.2)
DEL PEAK 13(9P23) MUTATED	143	65	0.2 - 109.9 (36.1)
DEL PEAK 13(9P23) WILD-TYPE	347	93	0.1 - 111.0 (34.6)

Figure S11. Get High-res Image Gene #25: 'Del Peak 13(9p23) mutation analysis' versus Clinical Feature #1: 'Time to Death'

'Del Peak 13(9p23) mutation analysis' versus 'PATHOLOGY.T'

P value = 1.32e-05 (Fisher's exact test), Q value = 0.003

Table S12. Gene #25: 'Del Peak 13(9p23) mutation analysis' versus Clinical Feature #5: 'PATHOLOGY.T'

nPatients	T1	T2	T3	T4
ALL	242	64	176	11
DEL PEAK 13(9P23) MUTATED	50	15	74	5
DEL PEAK 13(9P23) WILD-TYPE	192	49	102	6

Figure S12. Get High-res Image Gene #25: 'Del Peak 13(9p23) mutation analysis' versus Clinical Feature #5: 'PATHOLOGY.T'

'Del Peak 13(9p23) mutation analysis' versus 'PATHOLOGICSPREAD(M)'

P value = 0.000876 (Fisher's exact test), Q value = 0.19

Table S13. Gene #25: 'Del Peak 13(9p23) mutation analysis' versus Clinical Feature #7: 'PATHOLOGICSPREAD(M)'

nPatients	M0	M1
ALL	417	76
DEL PEAK 13(9P23) MUTATED	109	35
DEL PEAK 13(9P23) WILD-TYPE	308	41

Figure S13. Get High-res Image Gene #25: 'Del Peak 13(9p23) mutation analysis' versus Clinical Feature #7: 'PATHOLOGICSPREAD(M)'

'Del Peak 13(9p23) mutation analysis' versus 'TUMOR.STAGE'

P value = 5.35e-06 (Fisher's exact test), Q value = 0.0012

Table S14. Gene #25: 'Del Peak 13(9p23) mutation analysis' versus Clinical Feature #8: 'TUMOR.STAGE'

nPatients	I	II	III	IV
ALL	238	52	123	80
DEL PEAK 13(9P23) MUTATED	48	11	49	36
DEL PEAK 13(9P23) WILD-TYPE	190	41	74	44

Figure S14. Get High-res Image Gene #25: 'Del Peak 13(9p23) mutation analysis' versus Clinical Feature #8: 'TUMOR.STAGE'

'Del Peak 14(9p21.3) mutation analysis' versus 'Time to Death'

P value = 2.03e-06 (logrank test), Q value = 0.00047

Table S15. Gene #26: 'Del Peak 14(9p21.3) mutation analysis' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	490	158	0.1 - 111.0 (35.2)
DEL PEAK 14(9P21.3) MUTATED	152	72	0.2 - 109.9 (31.5)
DEL PEAK 14(9P21.3) WILD-TYPE	338	86	0.1 - 111.0 (36.2)

Figure S15. Get High-res Image Gene #26: 'Del Peak 14(9p21.3) mutation analysis' versus Clinical Feature #1: 'Time to Death'

'Del Peak 14(9p21.3) mutation analysis' versus 'PATHOLOGY.T'

P value = 9.4e-08 (Fisher's exact test), Q value = 2.2e-05

Table S16. Gene #26: 'Del Peak 14(9p21.3) mutation analysis' versus Clinical Feature #5: 'PATHOLOGY.T'

nPatients	T1	T2	T3	T4
ALL	242	64	176	11
DEL PEAK 14(9P21.3) MUTATED	51	14	81	6
DEL PEAK 14(9P21.3) WILD-TYPE	191	50	95	5

Figure S16. Get High-res Image Gene #26: 'Del Peak 14(9p21.3) mutation analysis' versus Clinical Feature #5: 'PATHOLOGY.T'

'Del Peak 14(9p21.3) mutation analysis' versus 'PATHOLOGICSPREAD(M)'

P value = 6.93e-05 (Fisher's exact test), Q value = 0.016

Table S17. Gene #26: 'Del Peak 14(9p21.3) mutation analysis' versus Clinical Feature #7: 'PATHOLOGICSPREAD(M)'

nPatients	M0	M1
ALL	417	76
DEL PEAK 14(9P21.3) MUTATED	113	39
DEL PEAK 14(9P21.3) WILD-TYPE	304	37

Figure S17. Get High-res Image Gene #26: 'Del Peak 14(9p21.3) mutation analysis' versus Clinical Feature #7: 'PATHOLOGICSPREAD(M)'

'Del Peak 14(9p21.3) mutation analysis' versus 'TUMOR.STAGE'

P value = 3.19e-08 (Fisher's exact test), Q value = 7.6e-06

Table S18. Gene #26: 'Del Peak 14(9p21.3) mutation analysis' versus Clinical Feature #8: 'TUMOR.STAGE'

nPatients	I	II	III	IV
ALL	238	52	123	80
DEL PEAK 14(9P21.3) MUTATED	49	10	52	41
DEL PEAK 14(9P21.3) WILD-TYPE	189	42	71	39

Figure S18. Get High-res Image Gene #26: 'Del Peak 14(9p21.3) mutation analysis' versus Clinical Feature #8: 'TUMOR.STAGE'

'Del Peak 15(10q23.31) mutation analysis' versus 'PATHOLOGY.T'

P value = 0.00045 (Fisher's exact test), Q value = 0.098

Table S19. Gene #27: 'Del Peak 15(10q23.31) mutation analysis' versus Clinical Feature #5: 'PATHOLOGY.T'

nPatients	T1	T2	T3	T4
ALL	242	64	176	11
DEL PEAK 15(10Q23.31) MUTATED	31	10	43	6
DEL PEAK 15(10Q23.31) WILD-TYPE	211	54	133	5

Figure S19. Get High-res Image Gene #27: 'Del Peak 15(10q23.31) mutation analysis' versus Clinical Feature #5: 'PATHOLOGY.T'

'Del Peak 16(13q13.3) mutation analysis' versus 'Time to Death'

P value = 0.000848 (logrank test), Q value = 0.18

Table S20. Gene #28: 'Del Peak 16(13q13.3) mutation analysis' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	490	158	0.1 - 111.0 (35.2)
DEL PEAK 16(13Q13.3) MUTATED	75	34	0.1 - 89.4 (28.5)
DEL PEAK 16(13Q13.3) WILD-TYPE	415	124	0.1 - 111.0 (36.3)

Figure S20. Get High-res Image Gene #28: 'Del Peak 16(13q13.3) mutation analysis' versus Clinical Feature #1: 'Time to Death'

'Del Peak 16(13q13.3) mutation analysis' versus 'PATHOLOGY.T'

P value = 1.3e-05 (Fisher's exact test), Q value = 0.003

Table S21. Gene #28: 'Del Peak 16(13q13.3) mutation analysis' versus Clinical Feature #5: 'PATHOLOGY.T'

nPatients	T1	T2	T3	T4
ALL	242	64	176	11
DEL PEAK 16(13Q13.3) MUTATED	28	3	39	6
DEL PEAK 16(13Q13.3) WILD-TYPE	214	61	137	5

Figure S21. Get High-res Image Gene #28: 'Del Peak 16(13q13.3) mutation analysis' versus Clinical Feature #5: 'PATHOLOGY.T'

'Del Peak 16(13q13.3) mutation analysis' versus 'TUMOR.STAGE'

P value = 0.000324 (Fisher's exact test), Q value = 0.071

Table S22. Gene #28: 'Del Peak 16(13q13.3) mutation analysis' versus Clinical Feature #8: 'TUMOR.STAGE'

nPatients	I	II	III	IV
ALL	238	52	123	80
DEL PEAK 16(13Q13.3) MUTATED	27	2	27	20
DEL PEAK 16(13Q13.3) WILD-TYPE	211	50	96	60

Figure S22. Get High-res Image Gene #28: 'Del Peak 16(13q13.3) mutation analysis' versus Clinical Feature #8: 'TUMOR.STAGE'

'Del Peak 17(14q31.1) mutation analysis' versus 'PATHOLOGY.T'

P value = 0.000106 (Fisher's exact test), Q value = 0.024

Table S23. Gene #29: 'Del Peak 17(14q31.1) mutation analysis' versus Clinical Feature #5: 'PATHOLOGY.T'

nPatients	T1	T2	T3	T4
ALL	242	64	176	11
DEL PEAK 17(14Q31.1) MUTATED	83	35	96	4
DEL PEAK 17(14Q31.1) WILD-TYPE	159	29	80	7

Figure S23. Get High-res Image Gene #29: 'Del Peak 17(14q31.1) mutation analysis' versus Clinical Feature #5: 'PATHOLOGY.T'

'Del Peak 17(14q31.1) mutation analysis' versus 'PATHOLOGY.N'

P value = 0.000113 (Fisher's exact test), Q value = 0.025

Table S24. Gene #29: 'Del Peak 17(14q31.1) mutation analysis' versus Clinical Feature #6: 'PATHOLOGY.N'

nPatients	0	1
ALL	228	18
DEL PEAK 17(14Q31.1) MUTATED	96	16
DEL PEAK 17(14Q31.1) WILD-TYPE	132	2

Figure S24. Get High-res Image Gene #29: 'Del Peak 17(14q31.1) mutation analysis' versus Clinical Feature #6: 'PATHOLOGY.N'

'Del Peak 17(14q31.1) mutation analysis' versus 'PATHOLOGICSPREAD(M)'

P value = 0.00101 (Fisher's exact test), Q value = 0.22

Table S25. Gene #29: 'Del Peak 17(14q31.1) mutation analysis' versus Clinical Feature #7: 'PATHOLOGICSPREAD(M)'

nPatients	M0	M1
ALL	417	76
DEL PEAK 17(14Q31.1) MUTATED	171	47
DEL PEAK 17(14Q31.1) WILD-TYPE	246	29

Figure S25. Get High-res Image Gene #29: 'Del Peak 17(14q31.1) mutation analysis' versus Clinical Feature #7: 'PATHOLOGICSPREAD(M)'

'Del Peak 17(14q31.1) mutation analysis' versus 'TUMOR.STAGE'

P value = 2.36e-05 (Fisher's exact test), Q value = 0.0054

Table S26. Gene #29: 'Del Peak 17(14q31.1) mutation analysis' versus Clinical Feature #8: 'TUMOR.STAGE'

nPatients	I	II	III	IV
ALL	238	52	123	80
DEL PEAK 17(14Q31.1) MUTATED	79	25	68	46
DEL PEAK 17(14Q31.1) WILD-TYPE	159	27	55	34

Figure S26. Get High-res Image Gene #29: 'Del Peak 17(14q31.1) mutation analysis' versus Clinical Feature #8: 'TUMOR.STAGE'

Methods & Data

Input

Copy number data file = All Lesions File (all_lesions.conf_##.txt, where ## is the confidence level). The all lesions file is from GISTIC pipeline and summarizes the results from the GISTIC run. It contains data about the significant regions of amplification and deletion as well as which samples are amplified or deleted in each of these regions. The identified regions are listed down the first column, and the samples are listed across the first row, starting in column 10.
Clinical data file = KIRC-TP.clin.merged.picked.txt
Number of patients = 493
Number of copy number variation regions = 30
Number of selected clinical features = 8
Exclude regions that fewer than K tumors have alterations, K = 3

Survival analysis

For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene cnvs 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 cnvs 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

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

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)

[5] GISTIC_version2

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